There are plenty of places to buy Gundam (assuming it's that Haro you want) merchandise in Tokyo without going all the way out to a museum if you don't want to.
Yodobashi Akihabara had a huge Gundam section last time I was there. Yamashiroya in Ueno has a fairly decent selection. LAOX Akihabara is supposedly quite good, but can't vouch for it myself. I also hear rumours that it's closed very recently, but this could be wrong.
I hesitate to recommend Nakano Broadway, but only because I don't remember seeing that much Gundam there. It's extremely worth a visit, but I wasn't looking for Gundam, so may just have missed it.
There's a very spiffy blog post on most of these stores here:
Tokyo Toy Shops | endless rambles