I live in Santa Clara a short 10 minute drive from SJC. This is complicated, but if you can go on line and get the CalTrain schedule you could take it all the way to the Embarcadero then grab a taxi to the pier.
Here is what I would do. Take a taxi from the airport to the Sunnyvale Cal Train Station (everyone knows where this is that lives in the area.) Then take the CalTrain all the way till the end where it stops at the very last station which is right next to the SBC Ball Park.
From there take a taxi to Pier 35 where you board the boat. It is a short taxi ride.