We had toured San Juan on our previous cruises, so we didn't book any excursions. We decided to walk around San Juan and returned to the ship.
I would recommend that you go up to the port or left side on the 14th deck and take pictures as the ship sails into port in San Juan. It is a great opportunity to capture beautiful pictures of the old fort.
In St. Maarten, we booked a private speedboat tour through Soualiga Destinations with Captain Bob (email@example.com). It was the highlight of our cruise and a great way to tour St. Maarten. For great reviews, go to Soualiga Destinations on Trip Advisor.