Out of all those, I've only been to Chakanaab and it was wonderful. At the time, (before the last hurricane) they offered the dolphin swim, which I absolutely loved. I'm not sure if they finally have that up and running.
The rest of the park is beautiful, good snowkeling, etc.
Its also easy to take a cab there from the pier, not far away, but too long to walk. If you have enough time, the shopping in town is decent too.
I loved Punta Sur. They have crocodiles you can feed. Some mayan ruins, a beautiful old lighthouse and great snorkelling. We went there a couple of years ago on a Carnival Tour (eco jeep and snorkel tour) and when we return to Cozumel in March we are going to rent a vehicle and drive out there again. I can't recall where I found it but on one of the Cozumel websites I found a discount coupon for admission into some of the eco-parks you were mentioned in your post.
No Punta Sur is directly south on the main highway from the port of Cozumel. Cozumel has a main road that circles the island and so if you leave the port and hang a right on the main drag, you should have no problems finding it. I would definitely find a good map though beforehand, just so you have an idea where you're going. I think the website was something like cozumelinsider dot com.
Quick question for you (Showcat) about Costa Med. What was your impression of the ship, service, etc... I actually went so far as to book it once then chickened out and changed my mind to something else. Also where in Illinois are you?