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To start, I'd stay in Marathon if you want to be near good off the beach snorkeling. Two nice Mom & Pop type motels are Blackfin and Sea Dell. They are owned by the same outfit and we stay at Blackfin when we can and the other if Blackfin is full. There are other chain hotels in Marathon as well.
If you are just snorkeling off the beach and not collecting, Bahia Honda State Park is great! And they have a charter boat that goes out to Loe Key twice a day. If you've never been to the big reef, it's certainly worth the trip! Off the ocean side beach is terrific and/or rent a kayak there and go snorkel out at Little Bahia Honda (less than 1/4 mile off shore).
The other easy place to go, whether you are collecting or not is the Horseshoe. It's always good and it's more protected from the prevailing winds and waves than Bahia Honda. If the winds and waves are light, the ocean side across the island from the Horseshoe can be well worth a visit, but it's more commonly kind of rougher there than any of the other places.
There are lots of maps and aerial photos with my doodling outlines of where the best areas are, in this thread.
We will be there the 2nd week in September (assuming the weather looks good). We are lucky enough to be close (and retired), so if the weather looks bad, we can cancel and reschedule.
If you have any questions, I'm happy to try an help.
Greatly appreciate the advice - and the motel recommendations!