If you didn't live where the track died, then you would still say BART is more reliable. I've noticed BART is less reliable in the edges vs the core of SF, berkeley and downtown oakland
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.
The reason why there probably isn't any service from jack london square is because it's faster to get to a bart station by bike or similar and then take the BART.
As for vallejo, there looks like there is a ferry service for some reason according to google maps: https://www.google.com/maps/place/38%C2%B005'59.8%22N+122%C2...
The ferry terminal in San Francisco, on the embarcadaro, is about as central as central gets ...
Yes, there is a Vallejo ferry which goes right to the center (see just above) of San Francisco.