We were on Celebrity Galaxy 12/2001 and stopped at Margarita Island. At that time, we read it was best to do a ship shore excursion, as that port was "new" and not many people knew much about it. We did a FANTASTIC tour that incorporated some gardens, a tropical labyrinth, some shopping, and a boat tour of La Restinga. We got to hold a huge snake and a cute little monkey named Poncho. The boat tour of La Restinga was very interesting. It was a fairly cheap excursion at that time. We had also read (back then) of the taxi drivers not getting people back on time, which is the reason we chose a ship excursion. If we didn't make it back, then the ship is responsible for us.
Regarding St Thomas and St John: I highly recommend St John. Not because I married there on a cruise in March, but because we vacationed there last Thanksgiving for the week. St John is beautiful, and the north shore road has beach after beach after beach. Our favorite is Cinnamon and Little Cinnamon. Free, very long sandy beach, facilities, and very good snorkeling. It is just a little past Trunk. www.vinow.com
has great descriptions of each beach on St John. Plus, you can walk to some ruins right across the street from Cinnamon. Some of our pictures from St John: www.cmgoddard.com