We love Pancho's Backyard.
It is a restaurant in a courtyard of a large store called Los Cinco Soles. The cruise director will probably mention it in his shore excursion talk. When you are walking down the street in the main town in Cozumel with the water on your left and the shops on your right, it'll be several blocks up on your right. Los Cinco Soles also has some very nice stuff.
The food at Pancho's Backyard is outstanding. Watch out for the margaritas, they pack a wallop.