JR Pass

Hi, I am travelling to Japan from 14 to 22 April and will explore Tokyo and Kyoto during the trip.

I have purchased JR Pass but not sure when I should start to use?

I will arrive Narita at 1pm, if I decide not to use JR Pass for my 1st day, which cheaper way I can go for the trip from Narita to Tokyo?

I plan to go Mt. Fuji on the 2nd day, I should use JR Pass or to buy Hakone Pass?

Directions from Narita Airport to Tokyo:
http://www.japan-guide.com/e/e2027.html

As for Mt. Fuji it depends. Hakone is just one area where you might /might not see Mt. Fuji depending on weather conditions. Hakone is a fantastic place to visit either case.

Just depends on what you mean by "Mt. Fuji". There are many ways to see it, and ways to get to it.

As stated there is seeing Mt Fuji or going to it. You can usually see it from the Hakone area. It is very much weather dependent as it frequently gets clouded over. You would use your JR pass to get to Odawara and purchase the Hakone pass there. The Hakone pass will then let you travel on everything in the area. You can get back to Mishima by bus and take the shinkansen back to Tokyo from there.

I wanted to see Mt.Fuji closer so that I can take nice picture, also I wish I can go atleast 5th station. I believe the view of Mt. Fuji here will be better than Hakone...

Is that mean I cant make it if I go Mt. Fuji follow by Hakone area? Or I can only go either one unless I stay a night at Hakone? Or I can total not to go Hakone?

Fuji san is very ironic. You tend to take better picture from a distance than being close to it. I took an excellent picture from the Shinkensan (osaka to Tokyo) couple days ago through the train window. It was so clear and not much of cloud/smoke at the top but only the snowed mountain top.

Concerning JR Pass, I don't know how you plan the rest of your trip after Hakone, so I cannot suggest exactly when you should activate it, but you want to make sure that the round trip between Tokyo and Kyoto falls within a 7-day period.

For example, seeing that you have 9 days, if you fly in on Day 1, then travel to Hakone on Day 2, then go to Kyoto on Day 3, then returning to Tokyo on Day 8 and going to Narita and flying out on Day 9, you could maybe purchase use Nex & Suica package upon arrival at Narita (Narita express ticket plus prepaid Suica card for in-Tokyo use at a discount).

- Then for Day 2, you can either buy separate non-JR (Odakyu) round trip ticket starting from Shinjuku to Hakone, and then activate the JR Pass on Day 3 so you can use it for the round trip to/from Kyoto and the ride back to Narita on your last day as well.

- Or you can activate if on Day 2 and use it to get to Odawara on JR train, and then use local transportation to get to Hakone from there, and for the last day to Narita use a different means of transport, such as Keisei railway (either Skyliner or Limited Express).

Mt. Fuji can be viewed from Hakone area, Lake Ashi I believe (if the sky is clear, that is). If you get to 5th station, you are halfway up the mountain so you won't be able to "see it" from a distance :)