Try this link if you go past Akihabara, and i recommend you do!
Most figure/hobby stores have at least a few TFs, but the best ones to visit are:
Yodobashi Camera.. i think it was 6th floor; Movie TF's, Encore's and Henkei.
Radio Kaikan.. this is a building housing heaps of smaller stores on different levels; all together, you could probably find most recent Japanese TF's and a few older ones.
Liberty Store #7.. must-visit store, 1st floor has got about 6 glass cabinets of TF's, mostly used, from all era's and a giant 1.5m Optimus statue!
Mandarake... ABSOLUTE must have if you're into G1, 2 full rows of glass cabinets, TF's from all era's, about 50% of it is Japanese G1. Make sure your wallet is prepared, though just seeing it is fun itself :) It's on the top floor, but only the right hand elevator gets to the top floor!