We didn't do an excursion here, so there wasn't really much to do. We enjoyed just walking into town and doing some shopping. It would be easy to go to the beach there since there are so many people offering to rent you chairs with drinks, etc. We just didn't end up doing that.
We took a taxi to the ferry port and went over to St. John on our own. We then took a taxi to Trunk Bay and did some swimming there and used the facilities. We learned that you could get off just before Trunk Bay if you wanted to just go to a beach without a shower and bathrooms, etc. There was a fee for getting into the beach at Trunk Bay ($4 each) which we weren't prepared for. We just barely had enough cash with us for the taxis, ferry and fees for the beach. I thought I would be able to use a credit card for the ferry, but that wasn't the case. Just be sure to bring along a lot of cash if you do this independently. It may be worth going on an excursion through the ship for that reason. Trunk Bay is absolutely fabulous though. It is well worth going over there. I would definitely do that again on my next trip to St. Thomas!
This is another stop that really doesn't have much to offer other than Atlantis. I had been there before, so we just opted to get off the ship and walk around. I didn't realize that there is a beach within walking distance of the ship. It certainly isn't as nice as most of the beaches but it would work if you just wanted to get out in the sun and not pay for a taxi, etc.