The Good: We went on our own, caught a cab with several people (we did not know) from our ship to Red Hook on St. Thomas. From there we went by ferry to St. John, and another cab to Trunk Bay. St. John is largely national forest, less than 10% developed, and looks like the Caribbean was meant to--no venders! You will not save money doing this, A ship's tour to Trunk will cost about the same as the cab/ferry/cab combo, but you will have control over when you leave. After everyone was herded back to the ships we stayed at least another 1-1/2 hours before we headed out, with plenty of time to spare before sailing time (my daughter and I shopped for a couple hours on St. Thomas--we could have stayed at the beach longer yet but wanted to be sure to make it back). Trunk bay is so gorgeous! You can rent snorkel equipment there and snorkel a marked trail right from shore, or move over 50 feet and be on white sand as far out as you care to walk. There is a small admission 2-4 dollars if I remember, to enter the park. There is a decent concession there, and clean washrooms. The people were courteous and spoke English (you are in on a US Virgin Island). If you don't like Trunk grab another cab and go up the shore to Cinnamon Bay. St. Thomas is the shopping capitol of the world apparently, and I will shop at the Mall thank you. I came to see and do, not carry home! Friends took a sailboat on a private charter to a few snorkeling spots around St. Thomas and neighboring islands, and liked this even better than Trunk--small craft got in some really fun secluded places. You are in port a long time and can arrange things like this with minimal worry if you allow plenty of time to get back to the ship.
Also good: We went to Orient Beach on St. Marten. Very little nudity (we had two teenaged girls with) and mostly restricted to one end of the beach, but naked people did feel free to go for strolls and you WILL see them. The surf was high that day and my girls were too busy body surfing and jumping in the waves to worry. Also did this on our own: many many cabs outside cruise terminal on St. Marten. Driver agreed to return for our whole cabload (we 10 strangers pretty much agreed on a time we all could live with). He came back right where he said he would be, but beach is lousy with bars/restaurants. If by some freak of nature you can't see a cab and yours doesn't come back you will be able to call one with no problem. No one naked on Orient should have been, in my estimation--do some Pilates!
The bad: We tried to go horseback riding on St. Marten at Lucky Stables. We arranged weeks in advance via internet (checked references they gave us and also on chat sites) They were so far behind we could not possibly do the ride and make the ship. Very disappointed daughter, as well as cab fare ($20 one way) down the drain. Other family that shared our cab had waited on the "beach"--not anywhere you really want to hang out, rocky and not cool) for two hours for their turn and couldn't do it with the delay either. We would have stayed at Orient 2 hours longer. After wasting all the time and money we had to buy our pop and pringles from them while we waited for our cab.
The good: We have done many many trips on our own and always had a superior experience to the ship's over crowded offerings (I am not a big fan of being herded anywhere in a huge group) and Lucky Stables was our only strike out.