Unless you need to provision, I would skip the USVI and Tortola and go to JVD first to visit Foxys, White Bay (Soggy Dollar), and other points of interest. You can clear customs in Great Harbour. At least you could a few years ago. I doubt that has changed.
Do I detect a bias in Capt Tony's recommendations? Methinks, the man likes his beach bars! (But there's nothing wrong with that.)
Where to go depends on what you're looking for -- if you want to spend time in a small town with little to offer other than a well known beach bar, a harbor full of charter boats on $30 moorings, and lots of drunk yachties, then head on over to Jost van Dyke.
On the other hand, if you're looking for peace, quiet, natural beauty, great walks ashore, $15 moorings, great snorkeling....St. John's your place. Best spots are the bays on the south coast and Francis/Maho Bay on the north coast. In these bays it's possible to dinghy to some of the most beautiful beaches in the Caribbean and have dinner ashore in the inexpensive restaurant of the Maho Bay Campground. Watermelon Bay, also on the north side of St John is also a great place.
I'd also recommend Christmas Cove on the west side of Great St. James (?) Island on the SE corner of St. Thomas. Moorings here are free and it has some of the best snorkeling in the VI (around the small island between the mooring fields and at the north end of the cove.)
If you're looking for some "big city" action, anchor for a night in the harbor at Charlotte Amalie. Duty free shopping, several good bars and many good restaurants ashore. Old Danish-era architecture gives the place a nice feeling when there are not too many cruise ship passengers around.
Culebra is a fun stop for a night. (I recommend dinner by dinghy at Mamacita's on the canal just west of the bridge). Culebrita is also a good place to visit in settled weather, low winds, and no swell from the north.
Distances are manageable from the east end of PR
, if the trades aren't blowing very hard. My memory suggests that it's 20 miles to Culebra, 20 more to Charlotte Amalie, 12 more to St John -- all to windward.
On the way back to PR
watch out for the reef sticking out on the south side of Culebrita / SE side of Culebra. It has some of BR's bottom paint on it!
If you're up for Capt Tony's haunts, you can still clear in and out at Great Harbor, Jost van Dyke.