The Japan Rail Group currently does not offer any discounts to the Japan Rail Pass for wheelchair users. However, you can purchase the regular Japan Rail Pass.
See the “Accessibility” section on the JR East webpage to find out how to get assistance, what major accessibility features are available, and other specifics about using the trains and stations.
You can also find more information on accessibility in Japan on the JNTO website:
The staff at stations will always do their best to assist wheelchair users, however it is recommended to avoid peak commuter hours if possible, as the trains can be extremely crowded.