I believe St. Maarten is the better port to snorkel. I did the Rhino Rider Adventure back in December and we drove 2 person motor boats to a snorkel spot. The water wasn't the clearest, but the overall excursion and experience was great. I know Royal Caribbean has lots of snorkeling excursion options for St. Maarten.
I consider San Juan more of a historical port and usually walk around the streets.
I always bring my own snorkel (full face mask on Amazon) with me. Labadee had some cloudy water, but I didn't go to a specific area to snorkel. However, you wouldn't have to worry about it taking up your whole day or a large chunk of it as opposed to an excursion on a different island.
MelKaps got a reaction from ChessE4 in Snorkeling Labradee, San Juan or St. Marteen