Here is a list of favorites gathered from this forum and some other folks (some off the beaten track - OTBT).

The Indians
Jost - White Bay (west end)
Fallen Jerusalem
Anegada - Loblolly Bay, either end
The Dogs - esp. Great Dog & George Dog
Buttonwood Bay - west end of Great Harbour, Peter Island
Monkey Point on Guana Island
The Wreck of the RMS Rhone
Norman Island- the Caves and the promontory to west of Pirate's Bight
Alice's Backside - north side of Ginger Island
Cistern Point - Cooper Island
Long Bay on Virgin Gorda
Green Cay off Sandy Spit -
Salt Island, "Mans Head"
Great Camanoe off Marina Cay (Diamond Reef)
Diamond Cay
off-beach Gorda snorkeling: The Baths, Spring Bay , Nail Bay, Savannah Bay, Guavaberry, Mahoe Bay (probably the best)
off-beach sandy bottom snorkeling at Manchioneel Bay (Cooper) - rays & turtles !
Gorda: north side of Prickley Pear, the Anguila Cut, Eustacia Reef
Chromis Reef - on the west side of Cooper Island
Vanishing Rock - between Salt and Cooper Islands in a narrow passage
Loblolly Bay, Flash of Beauty - Anegada
Coral Gardens. Located Northeast of Dead Chest Island
Soldier Bay - Norman Island - around the tip of Norman Hill (a/k/a Spy Glass Hill)
"The Aquarium" - Nestled between the Baths and Spanish Town (Virgin Gorda )
rocky shore between the mooring field at Diamond Cay up to Green Cay on JVD
Brewer's Bay - left side in front of Nicoles; in the middle; & the reef by campground, Long Bay, Devil's Bay
west side of Sandy Spit, if no northern swell

Nice "best 10" list: http://bvinewbie.com/top-10-snorkel-sites-in-the-bvi/

A good diving & snorkeling web page here