The museum is in Mitaka, which is a bit outside of Tokyo proper, but only a few stops down on the JR Chuo Line from Nakano, not hard to get to at all. Tickets to the museum must be purchased either at a Lawson's in Japan, or at a designated travel agent outside the country. We bought our tickets through a travel agent here in Korea without problem.
You can't take photos inside the museum, which makes this post a little boring. There was one room that explained animation without words. They had various samples of how you can make things appear to be moving or appear to have depth when in fact there is no depth or movement. That part was fairly interesting. They also had an original animation (no dialogue, so it can be understood by anyone) that can only be seen at the museum. I think they periodically rotate the movie to encourage guests to come back again. The rest of the museum seems to be dedicated to showing sketches from various movies, show sample animator's desks, and showing copies of the storyboards for various movies.
It was interesting, but I feel a little let down. All signage was in Japanese, so I couldn't read any of the explanations for any of the exhibits. Though I was surprised at just how few foreigners were there on a Saturday. It was teaming with Japanese visitors though. Much more crowded than I expected since you have to reserve a time to come in. Anyway, if you're a Hayao Miazaki fan, and you have time, the museum might be worth it. If you're pressed for time, it might not be a priority for you. Perhaps going on a weekday might be better since the crowds should be smaller.