Great Stirrup Cay had decent snorkeling if you don't have high expectations. They had an artificial reef like structure installed to protect the beach. I haven't been there in over a decade, but I think it will fit your bill. Pro tip, snag a couple boxes of Cheerios from the buffet and open them up under water - the fish will swarm 🙂
We will be in Nassau the end of next month with our 7 and 5 year old and am interested in hearing about snorkeling opportunities.
We were at Atlantis in February. I don't think I would pay to bring my kids there. The water park isn't worth the charge - crowded and unorganized was our experience.