My husband and I stopped in Cozumel on a Princess cruise. We booked a discover diving excursion through grandcaymancruiseexcursions.com. They do excursions with local guides at many ports. We had a great time. Our guide was terrific and we spent less than our friends who booked though Princess. The best part was that we were not hung up in the cattle call getting off the boat.
My husband and I are not "tour" people and we really enjoyed this opportunity to see Cozumel as part of a small group (there were only 6 people in our party including the instructor). We are taking another Princess cruise in March 2009 and we will be looking to local guides when booking our excursions. My advice is to shop around and when you find something interesting start hitting the various message boards for posts from people who have booked through that company before. Many people forget to post on their good experiences but you can sure bet they will post on the bad ones! Have a great trip.