We did the trolley tour on our own in KW and then went to a new pirate museum, Pirate Soul, which was really cool. Our 5 1/2 yr old loved them! The Pirate Soul was about an hour. It had some authentic pirate stuff, including 1 of only 2 original Jolly Rogers in the world. Also, some interactive stuff.
In GC, we did the 2 1/2 hr Captain Marvins snorkle and visit to Stingray City. DS is still talking about it. For the snorkling part, the kids do need to be strong swimmers. DS swims but he was holding onto 1 of us most of the time since it's deep and can be wavy. He was able to stand on his own with the Stingrays.
Cozumel, we did the Chanaakab Sea Lion Discovery, not our favorite but nice. (We had a 1yr old with us too so we couldn't do anything really)
I definately recommend the Capt Marvins and the Pirate Soul for kids this age.