Hokkaido and Osaka may be a better bet for what you are looking for (but I wouldnt bet my horses on it).
Tokyo, especially the Akihabara area should still be enjoyable for a toy collector, if you are in the frame of mind of not getting anything but might delightfully chance upon something...
The main sources of G1 TFs there - Mandarake and Liberty Store do not have much. But then again, that depends on the completeness of your collection. Pics will be posted on my blog soon-ish, so you can gauge for yourself.