There's a terminal at Mare Island, and according to the weekend schedule 3 of the 8 daily trips to Vallejo also go to Mare Island, and 3 of the 8 daily trips to San Francisco also go from Mare Island. If it's big enough maybe they can make special arrangements for it. https://sanfranciscobayferry.com/vallejo-ferry-route

Edit: it would be necessary to make arrangements because the weekend trips are for getting from Mare Island to San Francisco, not the other way around. They should be able to adjust their schedule but I don't know if they will.