Don't believe any schedules on the Internet, they are rarely updated. Most ferries operate early or late afternoon, as most of their revenue comes from commuters and some cargo. Like already said, Red Hook or Marine Terminal will get you to St. John, and other ferries from there will get you to JVD. Red hook will get you directly to West End, leaves "around" 8AM where you can check in, and then hop a ride to JVD any number of ways. Coming back you ALWAYS go to St. John to check back in.
There are some companies that only operate from St. John to BVI, generally stop first in West End.
HTH, Tell Uncle Vinnie I said hello.