The Tokyo Metro Museum in Kasai covers the history and workings of Tokyo's subway system, with old train cars, models, signalling displays, and driving simulators. It is especially good for rail fans and families with children who want something more hands-on than another art or history museum.
The museum is outside the central sightseeing districts, so it makes most sense if you are already in eastern Tokyo or have a specific interest in trains. Allow about an hour for the exhibits.