Buy JR pass for posted itinerary?

Hello, my husband and I are arriving in Japan at the Haneda airport on March 6 at 4.55pm. We are planning to go to Kyoto the same day and stay in Kyoto until March 9. We are planning two days in Kyoto and a day trip from Kyoto to Osaka. We are looking to go to Tokyo from Kyoto on the night of March 9 and stay in Tokyo for 3 days (March 10,11,12) until our departing flight at 9am from Haneda airport on March 13. What JR rail pass should I buy for my itinerary?

March 6 - Arrive at Haneda Airport, need to travel to Kyoto since hotel already booked for March 6-9

March 7 - Day trip to Osaka and return to Kyoto hotel

March 8/9 - Explore Kyoto and then go to Tokyo March 9 evening

March 10/12/12/13 - Explore Tokyo

March 13 - Depart Tokyo from Haneda

Buy rail pass or no? if yes, which one, for example east/west etc.?

None

Buy a 14 day one

Some international flights tend to delay so you might better consider this. Your flight might land at 19:00 when it is somewhat difficult to go to Kyoto, since you must go through immigration, buy ticket etc. in unfamiliar circumstance. I would recommend to stay in Tokyo on 6th to 8th and then fly from Haneda to Itami (Osaka), stay in Kyoto on 9th to 11th and then fly back from Itami to Haneda on 12th to stay around the airport for the morning flight. Flight between Haneda and Itami is 74.13USD one way.

I suggest you consider getting the japanican ticket.
https://www.japanican.com/en/special/tours/shinkansen/index.aspx
It's much cheaper than the JR pass, plus you can ride the Nozomi trains with it and get there 30 minutes sooner. Even factoring in the regular fares between Kansai cities, you still come out ahead. And since you're going to be seeing Tokyo, you could cut back your daytime in Osaka. It would be a shame if you missed Nara - it has some of Japan's best sights.
https://goo.gl/K3RqXH

Regarding JR Pass, to buy or not: It will be a close call, you might break even if you use a lot for local travels (in Tokyo mostly, a little in Kyoto/Osaka). Note that there aren't too many JR lines running in Kyoto and Osaka. Just for the Shinkansen rides alone (Shinagawa [near Haneda airport] to Kyoto, and Shin-Osaka to Tokyo) the reserved fare come out to 27740 yen, vs 29110 yen for the JR Pass. You do have to ride lots of local lines to make up for the difference of 1370 yen, but that depends on your itinerary. Another factor most people do not include in calculation is the convenience - how much is it worth to you that you don't have to buy individual tickets every time you ride on a JR line? In Tokyo, you can utilize local JR trains a lot, but you would only have 3 days left on your pass to use. In Kyoto, JR trains are utilizable perhaps only to go to Arashiyama bamboo grove and Fushimi Inari Shrine. You can utilize it if you decide to go to Nara. In Osaka, JR train is even less utilizable.

Complicating the equation more is the limitation of JR Pass when riding Shinkansen. You can ride on Hikari and Kodama only, which are slower than Nozomi, and they don't run as frequently as Nozomi. So, the last Hikari from Shinagawa to Kyoto departs at 20:10. If arriving Haneda at 5:00pm, there should be enough time to catch it nominally. But like frog1954 wrote above, things can go wrong with flights/customs.

Japanican mentioned by Ken is worth considering, because it allows use of Nozomi.

Don't get a pass for this trip. From Haneda International to Kyoto is 13,490 including the leg to shinagawa for a non-reserved seat to Kyoto. You do not need the hassle of voucher exchange after a flight when getting to your hotel in Kyoto is the priority. The eVoucher doesn't seem like a good option because of timing and the exchange process. The Japanican website displays this current customer comment The offices were difficult to find at both stations, despite the instructions.
The return to Shinagawa/Tokyo is 13,000 yen, so while you might do an extra 3,000 yen of local trains, your savings are not going to be large.

Thanks for such great details folks. I do agree with the advice to buy japanican ticket but then if I wanted to do day trip to Osaka and Nara (both on one day) from Kyoto, should I then activate the 1 day unlimited subway and bus pass that comes with the japanican ticket? Although that would still leave me with having to buy individual tickets in tokyo for the 3 days there.
In a scenario where I would take Shinkansen from Shinagawa to Kyoto the first day, then do day trips to Osaka and Nara the third day and return to Tokyo 4 th day and then use the pass locally in Tokyo for the remaining of 5th, 6th and 7th day, I would assume it would pay off it's price wouldn't it? unless option 1 of japanican + local subway tickets each day for 3 days in Tokyo would be cheaper than JR pass. Arghhh so confused...

The JR Pass is not designed for local travel, so forget about getting one to help cover your time in Tokyo. Get an IC card - a reloadable public transport card. You can read about them in the Transport section of this website.

Honestly, it sounds like you need to do more of your own research, because you're asking very basic questions.

Okay so after all research, looks like the JR rail pass cost WILL PAY OFF afterall considering the breakdown below comes very close to the price of the pass itself:

NO JR Rail Pass Breakdown
- Haneda to Kyoto including leg to Shinagawa one way ticket - 14550 Yen
- Kansai thru 3 day pass (unlimited use of trains, subways and buses in Kansai region around Osaka and Kyoto) - 5200 yen
- Kyoto to Tokyo via Shinagawa one way ticket - 14140 yen
- Unlimited 3 day Tokyo Subway pass - 1500 yen
- Tokyo to Haneda airport using Limousine Bus - 280 yen
Total - 35670 yen (Combined cost for Shinkansen from Haneda Airport to Kyoto and trip from Kyoto to Tokyo, all local buses/subways/trains in Osaka, Kyoto, Tokyo as well as return from Tokyo to airport)

The JR pass does not covers the tokyo subway or kansai buses/private railways. so you cannot factor those pass costs into into your jr pass calculations.

Unlimited 3 day Tokyo Subway Pass might not pay off (unless you travel a LOT on subways and subways alone), and it will not be covered instead by JR Pass even if you chose to buy JR Pass (remember, JR Pass is for JR = Japan Rail = trains, not for subways and other private railways).
For local travel (within/around Tokyo, or within/around Osaka), I recommend to get a prepaid card (reloadable). That can be used on buses, subways, private railways, and JR lines.

I am not familiar with Kansai Thru pass, so I cannot comment on that.

Remember that there are two inconveniences of the JR pass:
- you need to queue at Haneda to get your actual pass -> takes time and you donft have that much, specially if there is a delay with your flight.
- you canNOT takeNozomi Shinkansen. They are the fastest but also the most frequent ones.

Ad well as other mentioned it is only valid on JR trains. Not other trains/buses/subway...

So you add up two somewhat time consuming thing on you lr arrival date to maybe safe a little bit.

The only reason to get a JR pass is if your long-distance JR travel costs definitely exceed the price of the pass in my opinion. Using it in any other situation may (or may not) end up saving you some money on local JR trains but likely not enough to justify the inconvenience of being bound to JR lines, having to go through ticket offices at often busy stations (and not all exits have offices), plus the risk of losing the thing and being out of pocket a not inconsiderable sum of money. Maybe for some people thatfs a decent trade-off to save a few hundred yen over a short trip, but for me itfs not worth it. Suica card plus individual Shinkansen tickets is more flexible and convenient.

Okay so after all research, looks like the JR rail pass cost WILL PAY OFF afterall considering the breakdown below comes very close to the price of the pass itself:
- Kansai thru 3 day pass (unlimited use of trains, subways and buses in Kansai region around Osaka and Kyoto) - 5200 yen
- Unlimited 3 day Tokyo Subway pass - 1500 yen

Bad math. To spend 5,200 yen in/around Kyoto is way too much. Your day trips to Osaka and Nara are about half of that, so to buy an expensive pass to justify a JRP is wrong. Most of your travel in Kyoto is not covered by the JR pass either.
Similarly, in Tokyo, just using the metro pass (not that great) only covers a portion of the rail network - practically you will use JR trains as well.
And, you can use non-reserved seats as those are cheaper. Picking a more expensive option to justify an expense is false economy. (You do know the first leg Haneda to Shinagawa isn't covered by the pass so deduct that piece too.)

Yes, you could get a 7-day JR pass and you might save a little. The real difference is the hassle and time for exchange and the fewer choices for your initial trip to Kyoto during the evening. That cost of your time and travel disruption has not been factored into your calculations. Ultimately, your choice.

Okay done making up my mind, not getting the JR pass. The exchange office at Haneda Airport closes at 6.30pm, I don't think I want to chance it. I would rather just buy one off tickets. I thank you all for so much help and advice you guys have provided. I feel much more confident going there now than I was a few days ago.
One more question, I am thinking of doing Osaka and Nara on first day, Hiroshima on 2nd day and Kyoto on 3rd day (Hotel is already booked in Kyoto for 3 nights and so I must come back to Kyoto each night). Spend the rest of the 4 days in Kyoto. Is that too much or doable with efficiency?

If you decide to go to Hiroshima then a rail pass is worth it. However, I really don't think you have the time.

You're arriving in Kyoto late on the 6th so you're not sightseeing then
The 7th is Nara and possibly Osaka
The 8th is Kyoto
the 9th is Kyoto but you must leave by around 19 or 20:00 for Tokyo unless you are literally staying at Tokyo Station, because you need to give yourself some time to make it to your final destination in Tokyo and you really don't want to be on one of the last trains. I think most people would consider two days in Kyoto itself not enough time, let alone the one day you would have if you tried to add Hiroshima.

I'm not sure where the 4 is coming, from. You have most of 3 days.

Good luck!