Folks in a wheelchair should approach a member of staff before getting on a train. The staff will quickly get some folks to prepare a ramp (
pictured here) and help you onto a carriage that has space for a wheelchair. They will inform the approaching train that a wheelchair is to be boarded and the train will wait any additional time needed for you to get on. They will also contact your destination station and staff will be waiting with a ramp at the exact carriage that you got on.
A wheelchair is called "Kuruma Isu" . If you want to get off at Shinjuku station, you would say "Kuruma Isu. Shinjuku ikitai"