Hi there, we just returned from the Eastern Caribbean on Jewel of the Seas, with the same ports of call you listed. We purchased all of our shore excursions from the ship, and NONE were overcrowded. In fact, they will stop adding people to the tour at a certain point. This is the only way to have true peace of mind that you are GUARANTEED to make it back in time for your ship to depart.
Plus, because they are guaranteed by the ship, if you have any problem at all with the tour, the ship will work with you to resolve it so you don't have to work directly with the tour operator for resolution outside of the U.S. This happened to us in St. Maarten where we signed up for a full-day tour, but were only given 2/3 of what we paid for. All 11 of us on the tour complained when we got back on the ship, and we all received a 50% refund within 3 days (while still on-board) from Royal Caribbean. Give your friends that example and that may convince them to book a GUARANTEED excursion from the ship.
In San Juan, I recommend just walking on your own through Old Town and up to the Fort. No need for a cab or to pay for an excursion.
In St. Maarten, recommendation is a tour to Orient Beach (clothing optional). We didn't do this tour, but it's supposed to be the best spot on St. Maarten. If Pinel Island's boat are operating, do the snorkeling there. If the boat operators at Pinel Island are still on strike, DO NOT sign up for this tour because the alternative location (Dawn Beach at Oyster Bay) is subpar for snorkeling.
In St. Thomas, recommendation is a tour to Magen's Bay, one of the top beaches of the world. Beautiful water and sand there. Beach lounge chairs cost $6 each to rent.
In Antigua, recommendation is a snorkel trip to Cades Reef. Beautiful scenery on the boat ride that goes 11 miles up the coast of Antigua.
In Nassau, recommendation is a Stingray Adventure or Atlantis trip. We swam with the stingrays, and had a blast, but next time around will visit Atlantis.
You'll have a blast no matter where you choose to go, but I highly recommend booking direct from the ship.
tj