The Transportation Museum has been moved to Omiya. According to the articles I've seen it's pretty incredible. Naturally, it was closed while I was there.
Also in the Tokyo area is the Edo Tokyo Museum. This is an absolute must! It's big and exhausting, but very well done. You won't want to miss this one.
On the border with Chiba prefecture is the Urayasu Folk History museum. The English audio guide comes very highly recommended. It's by the Urayasu government center almost straight north of Disneyland. It's actually closer to the Tozai line, though.
Over by Haneda airport is the Ota Folk History museum which is also said to be exceptional. These are museums the tourist rarely know about or get a chance to see.
Don't get suckered into seeing the view from Tokyo Tower unless someone else is paying. It's expensive and not as good as the free view from the government building in Shinjuku.
Hiroshima has the Yamato museum near the Kure shipyard. Take a translator with you if you go, since I hear that none if it is in English. Lots of displays on the famous ship, plus Leiji Matsumoto's epic comic (and TV series) "Space Cruiser Yamato". This was mangled in English as Star Blazers.
Osaka has a very nice transportation museum plus a Maritime Museum where you have to walk through a tunnel under the bay to get in.
Enjoy the trip. Let us know what you thought of the Chiba monorail.
Claude