We took a fantastic trip with New Horizons II last April. We actually were staying on St. Thomas - but, the boat did stop on St. John at Cruz Bay to pick up some other passengers who had scheduled to take the trip, as well.

So, don't hesitate to contact New Horizons II to see if they still provide that service. We also had to check into customs on St. John upon our return from BVI.

It was a great trip - we got to see The Baths in Virgin Gorda, had lunch at a great spot on Marina Cay - snorkeled off of Guana Island & enjoyed a bit of time on White Bay on Jost Van Dyke & had a painkiller from the infamous Soggy Dollar Bar.

All in all - a great trip.

Best of luck with your planning!

Flyaway Charters are power boats out of Coral Bay.
http://stjohnlinks.com/Charters/Flyaway/
They go to the BVI's.
There are a few charters that hit the BVI's, some out of Coral bay, somemout of Cruz Bay. I found them by Googling "charters St John" or something like that.

If you are going to the BVI the boats have to stop in Cruz Bay for customs. From my research on the same subject even though the boats originate in St. Thomas most would pick you up in Cruz Bay.
A lot of power boats require more than two people to take a trip to the BVI. A sailor from Coral Bay told me that if you want to go all the way to The Baths it is better to take a powerboat because of the time constraints with custom proceedures now. You have to get back before 5pm. Sailing depends upon what the weather is doing that day. If you just want to go to The Indians and Caves for snorkeling or to Jost Van Dyke you can find several sail boats listed above under both St. Thomas and St. John Daysails.

I called Flyaway Charters, a motor boat, but they want to go out with 6 people or have you pay for the private charter plus gas, and customs. If there is less than 4 of you going it is very expensive. I figured it would be around $700 for a day in the BVI once you add in gratuity and everything.

I only found one guy with a motor boat out of St. John that said he would take reservations for two people to go out to The Baths. He hadn't set his rate for the year yet when I talked to him several months back but my notes say it will probably be about $125 per person plus $20 customs. (plus gratuity) That seems to be the rate. The rate only seemed to vary by $5 to $10 between companies.
His web site is here:
http://www.lionindasun.com/

Cruz Bay Watersports by The Westin may book per person but I never called them. http://www.divestjohn.com/baths.html

We booked Stormy Petrel/Pirate Penny based on good reviews from this board. I believe they will pick you up in St.John/Cruz Bay

http://www.connectionsstjohn.com/piratesstormy.html
Call them at 340-775-7990

You could also use Connections st john to try and match you up with other travelers for a trip to the BVI to split the cost.

Good Luck.

Limnos also makes a stop to pick up passengers from St John, if that's what they offer is your 'cup of tea'