We did this cruise last year on the Triumph, and I will be on board the Freedom with you as well.
I have been to St. Thomas several times and there are many good excursions here - anything going to St. John or a catamaran is good. if you have time at the end of the day, take the cable car (can't think of what it is called)- it is located near the pier to the top of the island for some incredible views. For this trip i am thinking of doing the Bike/beach excursion.
In San Juan - depending on what your interests are....the ship docks relatively late, so in the past it is usually a shopping/dinner and drinks on a tropical island type event. I have found thathat the best coffee and vanilla are from Puerto Rico.
In St. Maarten there are also many good excursions. However, if all you want is beach, it is much, much cheaper to hop in a cab and head over to the French side. the shopping - jewellery, liquor - cannot be beat in Phillipsburg. Last year we took a cab to the Divi Beach resort on the Dutch side - much cheaper than doing it through Carnival - also we were able to stay much latet than the ship tour.
If you have any questions, please ask...