Mishelle,
San Juan: The ship docks near Old Town San Juan which is great to wander around in during the day (however, be careful there at night). Lots of old stores, homes with balconies/flowers, churches, etc. Get a drink at any of the local bars, walk up to the fort for some great pictures. My cousin has gone on the tour of the Rum factory and she enjoyed the tour.
St. Thomas: Get up early, catch a cab to the Red Hook Ferry. The ferry leaves hourly for a 15-20 minute ride to St. John. Once at St. John, catch a cab for a 5-10 minute ride to Trunk Bay (my choice for the most beautiful beach in the Carribean). Spend the morning there swimming, snorkling, and laying out. Leave about 12 or 12:30 when it starts getting crowded. Catch a cab back to the Red Hook Ferry, ride the ferry back to St. Thomas. Catch a cab to either: 1) back to the ship for lunch and to clean up, or 2) to downtown Charlotte Amalie for lunch and the best shopping in the Carribean. Shop (liquor, clothing, jewelry, electronics, linens, china, crystal, and just about anything else) until it's time to go back to the ship.
St. Maarten: Two choices, 1) negotiate with a taxi driver for a tour around the island. It's a beautiful island (one half is Dutch and one half is French). On the French side there is some good shopping, good restaurants. The Dutch side is a bit poorer and less inviting shops/restaurants. Maybe have the cab driver drop you off at Orient Beach (my wife's favorite beach and my second favorite), or choice 2) catch a cab over to Orient Beach and spend the day. Great beach that has sections that vary from a typical beach to topless beach, to clothing optional. However, no matter what you wear, or don't, you'll have a great time here with waverunners, bars, banana boats, etc.
All three islands are easy to get around using cabs, ferries, etc.
Steve