NAPS has locations around Japan. Carries a wide range of products from riding gear and accessories to bike parts. Also has a Service area for maintenance.
Mitaka NAPS has the widest range of Race Suits, mostly RS Taichi, Hyod, and Berik.
Ricoland has locations around the Tokyo Metro. Carries a wide range of products from riding gear and accessories to bike parts. Also has a Service area for maintenance.
Nirinkan - Driver Stand - Nirinkan has locations around Japan. Carries a wide range of products from riding gear and accessories to bike parts. Also has service area and some have bike sales.
Kushitani is a manufacturer of riding apparel and other accessories. Various locations in Japan.
Bosco carries Madif products, which includes Arlen Ness and Berik. They have a few locations around Japan.
Astro Products - Not a specialty store per se, but has many items that are like name brand products but made in cheaper places. Has many tools and other accessories. Bike stands, etc. Many locations around Japan.
Rental 819 - Several shops in the Tokyo Metro area. Some seem 'related' in that you can get a bike from another shops' site to a local one. Doesn't work for all of them though.
Japan Bike Rentals - Rental in Akasaka - Tokyo, also rents luggage and GPS units, and provides suggested touring routes