As far as music goes, it depends on what kind of music you are talking about. Big Japanese pop/rock acts? Jazz? Metal? The John Denver cover band? Shoegaze? Punk? There is so much music to be found and sometimes the venues are hard to locate. If you can be more specific about music type you might get more pointers.
You can try searching for some things here:
Metropolis Magazine | Japan's Number 1 English Magazine
And here:
Tokyo Gig Guide
My suggestion would be to read some reviews, listen to some of the bands at LastFM or something and then see who is touring when you get there.