AVOID THE BIG BOATS LIKE THE PLAGUE! At least that is what I would recomend.. I just got back from Coz about a month ago. We dove with Seaurchin dive and I cant speak highly enough of them, they are great. We averaged a 50min bottom time with them and went to allot of great places. There DM is a really nice guy and he know's the waters well. We had the mistfortune of diving with one of the cattle boats while we were down there and were lucky if we got a 35~40 minutes of bottom time on any dive.
Unfortunatly most of the operators who run the sixpacks probably wont go into town to pick you up, but its only a 5 or 10 minute taxi ride to the marina to get on your boat. But it cant hurt to ask.
here is there contact info..
www.SeaUrchinDive.com
Phone - from USA: 011-52-987-878-4888
Phone - from Cozumel: 878-4888
Cell - from Cozumel: 044-987-800-6797
P.s. Im not affiliated with these guys at all, I just like what they do and how they do it.