Forgot to ask, are there clean toilets at the major subways for kids? Changing diapers, cranky control, etc.
Try the toilets at the larger stations like Ueno, Tokyo, Shinagawa...
Smaller stations and metro subway stations might have less chance of diaper changing tables.
But generally speaking, the toilets in the train stations are pretty clean (in my opinion) and most of the time there's toilet paper supplied as well.