First, snorkeling isn't the greatest in St. Maarten. It's there, it's better than nothing, but it's nothing anyone would ever go to St. Maarten specifically for. If there is anything else that sounds good to you, like shopping, exploring the French side, relaxing beach day, parasailing, wave runners, Golden Eagle Catamaran (that does have okay snorkeling) etc... I'd recommend those first.
Both of these islands are VERY easy to do on your own with little risk as long as you build in safety times. Don't plan on getting back to the ship at 4:30 if it leaves at 5 - plan on 3:30 instead.
The snorkeling in St. Thomas is excellent. Best is to go over to St. John and snorkel there. The classic is Trunk Bay, but I also like Cinnamon or Honeymoon Beach as well. You can do Trunk on a ship's excursion, but your snorkeling time is pretty limited.
If you want a fun time and good snorkeling, there is one ship's exursion I do recommend and that is Captain Nautica's snorkeling. Fun!
You can also have good snorkeling right on St. Thomas at Coki Beach. Easy to take a taxi right over there and spend the day. They also offer a very good discover scuba program if you've ever wanted to explore scuba diving. If you book that, they'll come pick you up from the dock.