I went to the museum two weeks ago. Suginami is a short ride from Shinjuku, so put it on your list if you ever plan a trip to Japan

(and it's on the way to the Ghibli Museum too

). It's known as "anime town" because there are a few anime studios there apparently.
Pretty interesting. Though there isn't much info to be learnt if you lready know a bit about anime making (through DVD bonus making of for example), there are a few cool activities available.
You can use a drawing board and draw your own perfect looking Gundam (even if you're crap at drawing)
You can take the microphone and try to dub a small scene of Astroboy (you need to read japanese, though, and it's tough). Then you get the rendering on the screen with your voice.
There are videos explaining the process of anime making, a wall with all of anime listed in chronological order, there's a small theater where they show OVAs for a very small fee (like 50 Yen), and a media room full of DVD which you can watch for free (there are computers, just borrow, sit down and enjoy).
And at the moment, there is this Gundam 30th anniversary, with an exposition of models. Here are pictures of the exposition for those who are interested:
http://picasaweb.google.com/graou.hyoga/SuginamiAnimeMuseumGundam30thBirthday#