Is 7 day JR pass woth it?

With your itinerary alone as you make it, it will pay off if you use it to Kyoto and back and take the Narita Express from Tokyo to Narita Airport. But the Pass is almost useless in Kyoto - you can use it to go from Kyoto Stn to Arashiyama (western Kyoto) and that is about it. You'll need to pay for subways and/or buses to get around Tokyo, or use a taxi.
Personally I don't recommend going to the 5th station of Mt. Fuji - there is nothing there and no real scenery. Mt. Fuji looks much better from far away then partway up it.
You have 2 choices - to go to Hakone, or the Fuji 5 lakes area. Both have very good spots and you can see Mt Fuji well when the weather cooperates. Unfortunately, it often doesn't. At least if you go to Hakone there are many other places to see and things to do if it is cloudy or foggy. A JR Pass will not help much in seeing either place though. For more info, see:

http://www.japan-guide.com/e/e5200.html

http://www.japan-guide.com/e/e5206.html

http://www.japan-guide.com/e/e2358_008.html

http://www.japan-guide.com/e/e5210.html

http://www.japan-guide.com/e/e6900.html

http://www.japan-guide.com/e/e6905.html