Boats are fundamentally slow and cannot dock at the center of a city where most jobs are, but it's edges. Docking and boarding/unboarding is a minimum 5-10 minute process too. A really fast ferry goes at 30 knots, which is around 35 miles per hour. Often ferries are there because building the equivalent bridge or train doesn't meet the cost/benefit ratio, otherwise they are an inferior transportation option.
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...