On April 6th the Modern Transportation Museum is closing. The museum is no longer modern, but was a great place to take kids. It will be crowded, but if you have the chance to make it to Bentencho Station (弁天町駅) between now an the 6th I totally recommend it. Thankfully many of the exibits will be moved to the second JR West run train museum near Kyoto Station.
What made the Modern Transportation Museum so fun was all the great hands on exhibits. You could climb into the cab of an original first generation Shinkansen, reprogram a signboard, and open and close a real train door. The museum was also very affordable at only ¥400 for adults and ¥100 for children. I was only able to go twice, but I loved it each time.
Modern Transporation Museum / 交通科学博物館, a set on Flickr.