We went to a wall in Tokyo called B-pump
http://english.pump-climbing.com/gym/akiba/ . It was a good wall with plenty of problems to keep you entertained across all grades but was fairly expensive if I recall correctly. We also went to a wall in Kyoto which was insanely expensive (circa £25 each!) and it was absolutely dogsh*t.
As for crags, we went to Mitake. It's close to Tokyo, you can hire pads, and there's a few things to go at. It's not a particularly good destination but it is accessible from Tokyo. It gets very crowded at weekends! See my blog for more info:
http://www.unclesomebody.com/blog/?p=1156We didn't make it to Shiobara or anywhere else that looked good. Unless you speak Japanese or are going with someone who speaks Japanese then prepare for some interesting experiences!