here's a list of stores i shop at in japan. some are specialized, others more general. these sites are all mostly in japanese but can sometimes be navigated via their photos or google translate. feel free to ask for a better description of their gear; it helps me study...

scooter/bike stores:

Tokyo Parts (TP): the best scooter store of them all and the place i do most of my shopping. the only store in central tokyo specializing in aftermarket/custom parts for small scooters, and boy, do they specialize. if they don't stock what you want they'll happily order it for you. can't recommend them enough.

Ricoland: the bike department store that makes overseas visitors drool... hard. they have a huge range of parts, accessories and apparel.

Honda Japan: good for some OEM bike parts, and better for more fun gear like ASIMO toys, pins, and T-shirts

Moto-Jam: an online store* for small scooters and minibikes. one of the more reliable online stores.

GT-Moto Stage: an online store* with a good range of gear for all bikes and scooters, including riding clothes and other accessories. their site can be painful to navigate but they are pretty quick and reliable.

* requests for goods from online stores sometimes have a $12 fee for delivery (since most of them are outside tokyo). if parts are available, they will usually deliver to tokyo within a week. i try to use those stores only as a last resort, but many people are happy with the products they carry.

apparel stores:

A Bathing Ape online (i love BAPE, i don't know why)