Unfortunately, Japan isn’t very wheelchair friendly. Many stations don’t yet have elevators, but generally speaking, they have chair lifts that will take the chair up the stairs. As the previous poster said, the station attendants will take care of you.
The same goes for restaurants and hotels - they aren’t very wheelchair friendly. This is because space is so limited that a lot of businesses just don’t have the space for wheelchairs. It’s unfortunate, but the government has been working on it. Keep in mind, you will need to ask beforehand if your hotel room is wheelchair accessible. Otherwise you may be unfortunately and sadly surprised to find you can’t fit it though the door or into the bathroom.