We've visited St. John on a 40' cat for a dozen years. Our favorite snorkel spot is Salt Pond Bay. There are maybe 6 moorings, so it's quiet. As you enter, stay to port or starboard of the rocks in the center of the entrance. Since there are only a few moorings, arrive early before they fill, particularly because the other south-side bays fill as well. The next real fallbacks require traveling a fair distance to the west.
Snorkel the grass in the center of the bay, along the east side, then cross to the rocks in the center and return to the boat.
If you want a nice dinner spot, take the ten-minute walk up to Concordia, a small ecoresort. Carry a headlamp for the walk back.
The Concordia Cafe has a beautiful setting and views. Their curry chicken is excellent. More information at http://www.concordiaeco-resort.com.