Probably in order would be St. Thomas (we took the Sunny Liston Tour and that was very nice and reasonable in price.), San Juan and Bahamas.
As you mentioned, there is a beach close by to Atlantis, and I had read that you could walk there from Atlantis, but when we took the tour, it seemed like we would have had a distance to walk to the beach. The beach is FREE, which is nice.
San Jaun is beautiful also, as I really got to see it GOOD for the first time. As I said the 5 of us walked at least 6 - 8 miles, going up hill to the fort, and down to the beach. There are also horse/carriages to take you around also. When you're down at the beach, you look up at the high rock walls, and they are beautiful. There is also a very large tree (it looks like 3 threes have grown together), and it is beautiful.
Tortola is nice, although small, but it reminds me of St. Lucia with it's straw markets, which are nice, if you want to save money.
It has the Queens staircase which is nice to walk/see.
Hope this will help.
Walking back to the ship, and seeing the ship's front all in blue lights was beautiful too.