The National Museum of Nature and Science, Tokyo. Not only the exhibitions are impressive, the building itself is gorgeous as well. The museum is huge with its 6 floors filled to the brim with stuff to explore. Even just getting a short impression of everything will take half a day. Lots of games for children explaining various aspects of science.
Haven’t yet done this but they also have “Nights for Astronomical Observation”, for just 310 yen. From their website:
“Nights for Astronomical Observation are offered from 7:30 PM on the first and third Friday of each month from April through August, and from 6:30 PM from September through March (Available on clear nights, for 2 hours).
At Tsukuba Campus, Nights for Astronomical Observation are offered from sunset on clear nights, on the second Saturday of each month.”
Getting there is just a short walk from Ueno Station. From there, take the ‘Park’ exit. Admission fee is 620 yen. As usual with museums in Japan: closed on Monday.
Official (English) Website: http://www.kahaku.go.jp/english/