We were there last week and took our "first time on Cozumel friend" on an afternoon island tour. We just booked a taxi (van) for the three of us for the afternoon. We stopped at the ruins for an hour and a half, checked out some nice beaches, the arches, the blow holes, etc. with the taxi driver as our guide. Depending on the amount of daylight you have left, you can also hit one of the beach clubs.
The taxi driver was happy for the half day gig and the included guide (driver) being a local can't be beat.