We recently went to the Kyoto Kaleidoscope Museum, in part because I read in a guidebook that it was a good place to take kids. It was pretty cool but more appropriate for older kids. Basically it is a room with a bunch of artistic kaleidoscopes of various shapes and sizes-including one in the shape of a maiko. They also had kaleidoscopes that were projected onto the walls every hour on the hour. Some were quite beautiful, but the staff seemed a little anxious about S and J. The kids enjoyed it, but it held their interest only for a little while. One thing that might be fun would be to make your own kaleidoscope with kits they had there for Y350.
The nitty gritty:
Elementary and middle school: Y200
The museum website above has a map and a photo of the museum room.
It's not too expensive so I think it is worth a try, but it wasn't quite the hands-on-museum I was hoping for.