With regard to "must see" attractions at Cozumel, there are three:
>> The Mayan ruins at Tulum, located on the mainland,
>> The Ex Caret ruins and ecological park (which also offers snorkeling and swimming), also located on the mainland, and
>> The Mayan ruins at San Gervasio, located right on the island and combinable with a fantastic Mexican folkloric show.
Unfortunately, these attractions are mutually exclusive since the first two are full-day tours. The latter is a half-day tour, which would leave plenty of time for snorkeling or swimming at a location somewhere near San Miguel de Cozumel, where the ships call on the island.
By way of amplification, the Mayan ruins at Tulum are quite extensive and they reveal the rather advanced character of the Mayan civilization. The ruins at San Gervasio are more limited, but probably more significant since the island of Cozumel was a sacred place in the Mayan religion.
BTW, you might check on the Caribbean message board for additional information and comments regarding these ports of call since they tend to occur on Caribbean itineraries.