Hey I live just outside Tokyo.
I think the previous post is right about Kyoto. I just got back from a weekend trip there. It was great. You can rent a bicyle and go practically everywhere in Kyoto by bike.
But I have to disagree about Tokyo. There are a lot of fun things to do in and around Tokyo. For example there is Nikko which has great temples and the 3 monkeys. Mt. Fuji, Hakkone, and not to mention all of the cool places in Tokyo. Like Harajuku, Shibuya, Akihabara... There is the Ghibli Museum. The museum features anime by Studio Ghibli for example Totoro, Sprited Away, or Howl's Moving Castle. And I guess I have to mention Tokyo Disneyland (although I've never been there!).
There is a lot to do in Japan.
This is the website for a local magazine. It will give you some info about what's happening in and around Tokyo if you decide to come. http://metropolis.co.jp/default.asp
have a good trip!