Tokyo Metro Museum (Tokyo Subway Museum): Another Tokyo Train Museum!
There's a small shop selling train goods and some Tokyo Metro specifics. A couple lines have their own merchandise too. Nine of the subway lines have their own mouse pads, for 500 yen each.
The Chikahaku (Underground Museum) is open 10:00-17:00 daily except Mondays and around New Year. If I'm translating accurately, the museum is open on the first two Mondays of August for summer vacation. Admission is 210 yen, though in April it will probably increase due to the tax increase. The website (in Japanese only) notes that the store prices will increase, but I didn't see any details on museum admission.
Access is simple; take the Tozai subway line to Kasai Station. Be sure to take a local train. Use the east exit and follow the signs. If you're coming from Tokyo, you'll need to walk back under the train tracks as the entrance is on the south side of the tracks.