Depends where you are in Japan, in Tokyo definitely hit up Akihabara, it's like a suburb dedicated to all things nerdy

To look through everything in Akihabara, set aside at least two full days and make one of them Sunday... thats when a lot of freaky people come out. Don't be afraid to head above the ground floor, you'll find a heap more stores. There's one particular store that is on the ground floor and has heaps of G1 stuff, loose and boxed.

I personally preferred Osaka for TF shopping. For anything that was current, they tended to be ~10% cheaper. Head over to Namba station and look for signs pointing to Denden Town or Electric Street... it's basically another Akihabara, but smaller, bout a day and a half will cover it. I found less G1 stuff here, but at the far end of the street there is a shop that dedicates a whole floor to TFs and carries a lot of rare stuff.

With all the stores that are there, make sure you shop around before buying as prices can vary a lot, even between stores that are right next to each other!

Hasbro stuff is pretty insanely priced... Classics were all the rage when I was over there, with Jetfires going for ~AU$100. Takara stuff is cheap as, so do your Takara shopping in Japan and Hasbro shopping in Singapore.