One of the best train museums in the world is located in Saitama, City, Japan.
The museum opened in 2007 by JR East. It shows the history of the railway in Japan by showing trains that were formerly in service. Steam and Diesel locomotives, retired Shinkansen, and trains built for only used by the Royal Family. What's unique is not only can you go inside the trains but you can view the train from underneath and they also show some of the 'guts'.
The museum has train driving simulators throughout and really shows the mechanisms of trains with the use of parts and models. It has one of Japan's largest dioramas.
It takes roughly three hours to visit including lunch at their restaurant. The restaurant is good with views of nearby operating trains and also an overview of the museum. There is also a playground outside for kids.