I have visited Tokyo and stayed in three hotels whilst I was a wheelchair user:

Strings Intercontinental, Shinagawa
ANA Tokyo Intercontinental
Sheraton Miyako (I noticed that this hotel in particular was very popular with other wheelchair users, I saw more here than at any other place I’ve ever stayed at)

All of these can be recommended for those in wheelchairs, but I’ll confirm that the Strings was particularly convenient.

If you do stay at the ANA Tokyo IC, please ensure that it is explained to you how to access the hotel at night once the main doors have been closed for the evening. At night guests are requested to access reception using a flight of stairs outside the building. However, there is what might as well be a secret elevator entrance through the ARK buildings next door. This elevator can be found inside a nearby car park.
As I said, make sure you have been made aware of this.

Yamanote line is very convenient and even stations which don’t seem to have elevators will have wheelchair access - such as Shimbashi. Some escalators have special functions so that they turn from a staircase into a moving platform. It’s very nifty, but does mean no other passengers can use the escalator whilst it’s being used to transport a wheelchair. As a courtesy, it would be best to avoid peak time travel for these smaller stations.
When entering a station you will generally be asked which stop you are getting out of. Station workers can help with getting onto the train if you need it and can be there to help you out at your destination. They can also offer route advice so that you stick to the most accessible routes and use the simplest interchanges.

Shiodome/Marunouchi* border area is a nightmare.My husband would push me nearly everywhere in the wheelchair and we were surprised and delighted to find out how wheelchair friendly Tokyo is. However, on one walk we went from the Strings up to Tokyo station and came to this area, it turned out to be our Waterloo.
It may be that the planners and designers have incorporated a rat maze of subterranean elevators and tunnels into this new urban development so that they comply with theoretical access standards but we couldn’t figure out where they were. I had to be carried over some of the pedestrian overpasses.
If that guy with the cardboard signs is still there in April, I’ll join him for a spell.
For an area built so recently it’s shameful!
Avoid.

The area where the ANA Tokyo IC isn’t a great one, but it is doable.

I hope your friend is fit, the wheelchair access is generally there, it just means lots of lengthy detours so a chair bound visitor ends up ‘walking’ double the distance that a fit pedestrian will need to. The other pain is having to queue to get in and out of every station.

More info written whilst it was still fresh here
http://www.flyertalk.com/forum/8680415-post16.html

*Not the Marunouchi area - please see post below