We always snorkel in ports. St. Thomas we normally take the ferry to St. John and a cab to Trunk Bay. On the island of St. Thomas itself, Magen's Bay, Coki Beach, and Sapphire Beach are nice. St. Thomas is famous for shopping. There is a tram that will take you to the top of the mountain for a beautiful view. There's Blackbeard's castle. The snorkeling around there is great. We've done sail/snorkels to Buck Island and Scott Taylor did one that went to St. John that he said was fantastic. In Antigua we did a sail/snorkel, and it may have been the wrong time of year (October/November), but the water was full of jelly fish. Scott Taylor posted about spending the day at Pineapple Beach and said it was great. There's plenty of shopping right where you dock. In Nassau, grab a cab to Atlantis in Paradise Island (right across the bridge). There's a public beach adjacent to the hotel that's really nice. There's also the Queen's staircase, the straw market, and there used to be a turtle farm (not sure if it's still there). What was the problem with the "find" feature? If you could let us know, we could take a look at it. Best wishes.
We went to Nassau and St. Thomas in October 07. Below is what we did. Never been to Antigua. Hope this helps.
Nassau: We took a taxi to Cabbage Beach. This is a free beach near Atlantis on Paradise Island. We had a great time. Rented 2 beach chairs for $15 for the day and had all you could drink rum punch for $10 each. Our teenage son also rented a jet ski for an hour.
St. Thomas: We took an island tour with Sunny Liston Tours for $25 per person. Sunny and his wife Gigi were GREAT. Went to Mountian Top and then to Sapphire Beach. Sunny will give you a choice of beaches to go to. I would not go back to Sapphire, I would choose Coki or Megans Bay.
We did the America's cup racing yacht in Nassau last year. It was lots of fun, but not quite as well run as the experience people have in St. Marten.
We took a cab to Red Hook on St. Thomas, and then a ferry over to St. John. We spent the day at Trunk Bay. This is a national park. Clean restrooms, concession, snorkel equipment for rent. Lots of sandy beach. A marked underwater trail for snorkeling. We didn't save any money doing this on our own, but spent the day there rather than the 2 hour window (after you subtract transportation times from the ship's tour) allowed by the packaged tour. It was easy and safe, many people from our ship did this--we shared a cab from the pier with several. The ferrys run hourly--not sure on the hour or the half--other people on this site posted a link to the schedule previously, so if you catch your cab in coordination with that schedule you can maximize the time. St. John is 90% undeveloped and looks like the Caribbean you have imagined. Check it out!
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Although it's been a few years now, we did go to Antigua on a cruise. I loved it, but then I enjoy history. We took an island tour that focused on some of the historic spots, particularly the old dockyard. Thought it was quite interesting. Some nice overlook spots on the higher ground there too, so some good photo ops.
Most of the suggestions on St. Thomas and Nassau were right on the mark....St. Thomas has some of the best Gold prices in the Caribbean...You don't have to go far from the ship to do a days worth of shopping...well, at least my wife doesn't....Take the tram to the top of the island....$18 but well worth it...and there is a bar and small restaurant on top.....very beautiful views....I was just in Antigua 2 weeks ago...great island to take a tour of the forts and Lord Nelson dockyard...Have a Smashing good cruise..