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 