jonhall put together a fantastic spreadsheet identifying details of most dive shops in Coz. "Finding the (Best) Dive Shop in Cozumel" is the first thread in the Cozumel forum and loaded with great info.
I agree with Zman96's comments, essentially all the reefs are south so your travel time is about the same via boat from northern marina or driving to southern marina to jump on the boat. Depending on which reefs you dive the total time vary 30-60 minutes as well. If you want to get back by noonish you probably should find a dive op that leaves by 7-8 am. I dive with ScubaLife Cozumel which leaves the southern marina at 9:00 am and gets back at 1:30 +/- 30 minutes. Your drive from the southern marina to where you are staying is probably 15-25 minutes depending on cruise ship tourists along waterfront. If you drive to southern marina avoid downtown, circle around on 65th Ave.