One alternative is AC Transit's transbay service, which I swore by for many years. Unfortunately the increase in road traffic has that option declining as well.
There has been talk in the past about a Berkeley Marina/Albany Bulb ferry, but to my knowledge there are no current plans. I haven't ridden the ferry many times from other places, but I'd like to think that having that as an option would get a decent amount of ridership as well as possibly reduce the load on the roads and tracks.
The lack of any ferry service connecting the East Bay between Jack London Square in Oakland and Vallejo is pretty surprising. Judging from the fact that a morning commute-time BART train starting in Richmond is typically standing room only by El Cerrito Plaza (third stop on the line), I'd say the demand for alternatives is definitely there, so there must be financial/political/engineering reasons that there are no ferries from other parts of the East Bay.