The Tokyo Subway Museum is all about the underground railways and opened in 1986.
Underneath the subway line 100m east from Kasai station on Tozai-sen to the east of Tokyo. Note Tozai rapid trains do not stop there.
The following are on display:
First subway car 1001, car 129
In addition there are simulators, exhibits and a shop.
Japanese Railway Society report with pictures
This was also featured in JRS's magazine, Bullet-In 33.