Ive posted something to a similar question in another thread, here the copy
General Prices and living cost
Prices and living cost in Japan
Gaijin House´s:
Home
the one i stayed (quite nice!)
Oakhouse | Guest House Tokyo, guesthouse, room rent in Japan
and a site with appartments so that you could see into the prices. They might have something reasonable but im not sure if you can rent it on a temporary visa:
Tokyo Apartments -Reasonable Apartment Accommodation Guesthouse
i heard alot of bad things about sakura house guesthouses, so dont stay there! Their apartments might be ok, havent heard about that, only guesthouses.