If its your first time to Japan, I would recommend Tokyo. I found it best to get a middle-end business hotel in Shinjuku, and explore Shinjuku thoroughly. That will set you back around a day and is most worth it as you can see many sides of this ward.
Spend the remaining days venturing around wards which are connected by the Yamanote-sen. Its a train line that goes in a loop around Tokyo and covers most of the tourist spots, except Disneyland. Drop by Akihabara, Shibuya, Harajuku. In fact I found it to be extremely homely and just dropped by any stop that seemed interesting.
Disneyland is a must

Go by rail. Cheaper.
If you have some spare time, Kamakura or Hakone is a must. Train ride to Kamakura from Shinjuku costs 980yen, forgot the details about Hakone. Kamakura is a beautiful township beside the sea, famous for its shrines and giant buddha. Influences of Nichiren's Buddhism can also be found here. Overall a quiat little town. Hakone is near Mt. Fuji, a more inland and forested location. If you go to either one, you must take the local train for a scenic ride through the towns!
Thats about all from me for starters... Just let me know if anyone wants to know more regarding the Tokyo-to region or train systems, I will be glad to help
