Shamelessly points to sig pic below.
It really depends on what you're looking for, aside from the combiner stuff that you mentioned. If it's nothing in particular, then I would just go into literally every store in Akihabara that looks like it may sell Transformers.
Another large toy centric area in Tokyo is Nakano Broadway. They have a number of shops in there that sell Transformers, but mostly vintage and or used.
For new toys, Yodobashi and Bic Camera are everywhere and they sell them. Toys R Us there's 2 locations one in Odaiba as previously mentioned, another in Ikebukuro.