I hear many people are loving Railway Museum in Omiya.
It's in Saitama Prefecture so you will need to travel about an hour from central Tokyo.
There is also Tokyo Metro Museum, in Tokyo
Your kids may like them :)
If it's in summer, JR does "Pokemon Stamp Rally" every year. Kids can get Pikachu paper sun visor and collect Pokemon stamps by traveling around Tokyo by trains.
Currently, Kyoto Municipal Subway runs the wrapping trains until the end of October. Inside and outside of trains are wrapped with "Ensemble Stars! ", "Code: Realize − Guardian of Rebirth", "time bokan TWENTY FOUR" and "Fate/Apocrypha".
And there are ‘Galaxy Express 999’ runs on the Seibu Ikebukuro Line in Tokyo. The train runs until March 2019, so you will have still time to see and ride.
Your kids will love them!