Highly recommend the CYOA option. Sure... as several have indicated - the ferry is part of the adventure. When I'm on vacation I don't really like "adventure". Here are some reasons you might consider CYOA:
1. It's six or seven minutes (depending on the red lights) away from the airport.
2. Nearly all of the boats are near new at present. These are not cookie cutter "charter fleet boats" - these are all boats custom built by their owners and placed into the hands of the folks at CYOA.
3. All of the boats are well maintained. I have chartered with them multiple times and have seen/used boats that were near new and boats that were close to being sent back to their owners. I have had zero problems with any of them. ZERO! But of course boats are boats and I'm willing to accept that they break because I'm fully confident I'll be back up and running very shortly via help from the competent folks at CYOA.
4. Much better/cheaper to provision on St. Thomas. In fact I rent an Avis car at the airport, move my crew, provision the boat and hand it back in at the float plane terminal next door to CYOA. That costs me something like 70 bucks. Then I put the meat in the freezer - yup... all of the boats I've had have a freezer.
5. The other posters seem to indicate that you'll spend an extra day on each end dealing with traveling to/from St Thomas to the BVI. Simply not true. I can leave CA and arrive West End in about two hours. However, the anchorages of St. John are spectacular. So what exactly is the hurry to get to BVI? Even if the ferry situation was all sorted out I would still pick up the boat in CA if possible.
6. I have the option to sail to the Spanish Virgins.

And I can think of several other reasons as well but that's enough.

I had the same miserable ferry experience as you may have had. You will see on this board that many recommend tacking on an extra day so you can overnight on St Thomas before catching your flight home the next day. Huh? I overnight in Maho Bay on St. John and bring the boat in, refuel, and I'm on the CYOA dock by about 10:00 leaving me plenty of time to clean up and catch my afternoon flight.

After several charters at CYOA I bought a boat and placed it into charter with them. My ownership of a boat may seem like a reason to dismiss my input. I'll leave that up to you but I can honestly say I would have the same exact input independent of my boat ownership. Give it a try - I don't see how you can possibly have anything to loose.