JR Pass or Flights?

My friend and I are planning a 2 week trip across Japan later this year. We're looking to spend a few days in Tokyo, Kyoto, Osaka, and Hokkaido. From the research I've done it seems like JR Pass is the way to go but my partner swears that we can get around cheaper using domestic flights. Is there any validity to what he's saying? Thanks.

The further the distance from Tokyo, the better flights look. You can get a LCC flight from Peach or Jetstar or even the big carriers like JAL or ANA for a fraction of what a JR Pass costs. And the savings in time will be directly proportional to the distance from Tokyo. Hokkaido (Sapporo) is only 1:30 hours by plane, but 6 hours by train, for example.

Depending on your exact itinerary, a JR Pass for trains may work out cheaper than flights. But for Hokkaido, I would definitely consider flying to save time, since you are not planning to stop off between Tokyo and Hokkaido.

My friend and I are planning a 2 week trip across Japan later this year.

What is the exact dates? In general flights are better, but for specific dates, it will be very expensive.

I wonder what "research" you've done. All you have to do is to search prices and compare. If your dates are too ahead of time to see exact prices, you can find out what flight season your dates belong to and estimate from there. And if one of you have flight miles, that would even allow you to fly cheaper.

By the way, prices and time is not the only fun parts of traveling. Traveling on land is entertaining on its own way, even though it's slower than flying. And the JR Pass will allow you to board some of the fastest trains while letting you enjoy the fields, the towns, the long tunnel, and the freedom of walking around. What transportation you use really depends on your priorities.

I assume you are a foreigner to Japan, I would advise you to look into the various airlines that offer these special "Experience Japan Fare". Not sure how much I can say without sounding like an advertisement, but I've flown Tokyo to Akita as an example for JPY 5,500 each way. Do a Google Search of the airline that is blue and white and do some price comparisons. Depending on the route, I do recommend flying. But if you have the JR Pass you might as well use it given it is not a Flex Pass.

As others have more or less said, you need to give your whole itinerary - where you land, where you leave, how long, etc. Flying makes tremendous sense going from Tokyo or Osaka to Sapporo. And the train from Tokyo to Sapporo will take closer to 8½ hours, not six.
There are the LCCs mentioned before, such as
http://www.jetstar.com/jp/en/home
http://www.flypeach.com/pc/en
but for Tokyo that would mean going from Narita. For ANA's Experience Japan Fare
http://ana.ms/20Xtf8t
you could use Haneda.

There are other passes offered by all the JR companies other than the "JR Pass" 7/14/21day. Those offer unlimited use of Nozomi and Mizuho services on the Sanyo Shinkansen for example. What I do is immediately upon landing in Japan, I take another domestic flight from the same airline to the furthest point away from Tokyo. I then use the regional pass offered by the local JR company and then fly back to Tokyo when I'm done with that part of Japan.

So for my upcoming trip, I'm flying to Kochi, using the 3 day pass to see Shikoku, then going to Okayama and using the 7 day Sanyo-San'In Area Pass and use it for all my Chugoku side trips. Once done with the area, I'll fly back to Tokyo from Hiroshima. Once in Tokyo, I'll get the 5day-in14 JR East-Tohoku Pass for my excursions to the Niigata and Tohoku areas from Tokyo proper. I haven't purchased a JR Pass since 2015, 7 trips ago....

One option would be to open jaw your trip.

Fly to Hokkaido (you may have to change planes in Tokyo), spend time there, activate a JR pass when you leave Hokkaido, visit all your other places before your rail pass ends, and end up in Tokyo before flying home.

I would do the train between Tokyo and Osaka/Kyoto, just for the major time and hassle savings. It's only 2.5-3 hours on the train and you will be getting on and off near city center, so no airport ground transfer needed. You also don't have to arrive early or go through security procedures and wait for takeoff.

I would fly to Hokkaido. It's 8+ hours from Tokyo or 11 from Osaka. You don't want to waste an entire day of your expensive vacation on the train, do you? Even if you saved 20000 yen, you've spent at least that on a hotel and food for the day you wasted. (But honestly if you book early on Peach or Star, it very likely will not cost you extra vs train)

Tokyo. Hokkaido (Sapporo) is only 1:30 hours by plane,
Flight time might only be 90 minutes to New Chitose airport, but that is certainly not Sapporo or the time required to travel that leg from Tokyo. I would count on four hours minimum - you have to get to an airport, check-in time, then get luggage and then onward to Sapporo itself. However, that is still shorter than the eight hours by train.
Plus, assesses if going to Sapporo is really worth it given the time/cost commitment to get there when there are many other locations closer/easier to get to that can easily fill weeks.