On our first cruise almost 9 years ago we arrived in Cozumel after two hurricanes. Things were pretty much a mess. We went out to San Francisco beach and had a great afternoon. During that time a fellow passenger lent me a mask and I snorkelled for the first time in the Caribbean here. Water was cloudy and ocean a bit rough due to the storms. I have heard since that this is still a nice beach and that swimming and snorkelling here can be a lot of fun.
For children, I'd really recommend either of the two underwater parks they have on the island, Chankanaab (very close to where the ship docks), and a newer one on the south eastern point (something like Carocol, but I'm not sure). Chankanaab seems to be the favorite.