Not too far from the Bonsai Museum is the Railroad Museum. Located in Saitama, the museum naturally attracts both historians and children and it's a quick trip from central Tokyo.
While I'm neither of those demographics, I genuinely enjoyed my visit here. Before getting up close and personal with larger-than-life trains, there is a tiny village where you can see several types of trains including one or two high-speed ones.
There are also a few simulator rides for children, although this was probably my favorite part. I suggest doing some research before arriving through because many of the information is only available in Japanese. Even so, you can still get a feel for what it was like to travel on some of these old trains.