Some others I have yet to visit are Yushukan (war museum inside Yasukuni Shrine), the Tobacco and Salt Museum in Shibuya, the Tokyo Subway Museum in Kasai, the Tokyo Metropolitan Police Museum in Kyobashi and the Tokyo Waterworks Historical Museum near (where else?) Suidobashi station.
Here is a useful but incomplete list of museums in Tokyo.
One GLARING omission is Nippon Copack's Hanger Museum in Asakusabashi.
Traditionalists may be slightly wary to call this a museum, in fact.