I suspect the Center for Independent Living in Berkeley can tell you a whole about this matter. http://www.cilberkeley.org/

By the way, I recently stayed at the historic Hotel Whitcomb on Market St. Vaguely dodgy area but I didn't mind and it is right by the Civic Center BART. http://www.hotelwhitcomb.com/main/WHITCOMB-Page.asp?p=1

I paid around $75 through a discount agency. http://www.quikbook.com/ I believe with a level in from Market and elevators this would be accessible.

PS I got the Whitcomb from Quikbook as one of their Secret Sale deals so I didn't know the hotel until after paying. This was a super price for SF in the Winter so I would expect to pay more now that Spring is here. Also, I believe BART has some sort of 60-70% discount for folks in wheelchairs but it can only be purchased at certain stations with real attendants, not those with just ticket machines.