I've been going to Cozumel for over 25 years now, and have never done a stay and dive package. In my opinion, you can almost always do better by going ala carte - select where you want to stay, then pick a convenient high quality Dive Op separately. I know that there are big fans on this board of some dedicated dive resorts, like Scuba Club Cozumel, Papa Hogs, or Blue Angel, all of which offer dive and stay packages. And there are some Downtown Dive Ops, like Blue XTSea (by reputation, an excellent Dive Op, and Christi, the Owner, is a frequent contributor to this Board), will put together some pretty decent stay and dive packages.
You can compare pricing for just Dive packages by looking at the websites of several operators. I looked earlier today to compare pricing, and Dive with Martin, a budget operator but still a very good Op (I've been diving with them several times, and have no complaints at all, and I really like a couple of its DMs), offers a 5-day 2-tank package for $305, plus the $3 per day Marine Park fee. While I personally prefer Aldora for its HP Steel 120 tanks, Nitrox in any tank size, very long bottom times, and longer SI at a beach club, Aldora is also near the top end in terms of pricing, while Dive with Martin is near the bottom, but still NOT a cattle boat operation. Dive with Martin leaves from its office at the shore end of the International Pier, and doesn't pick up Downtown, so you need to either stay near the Pier -Casa Del Mar, El Cid La Cieba, Park Royal (an AI, which I avoid on Cozumel because of the wealth of great restaurants), or Village Tan Kah, or take a taxi from downtown (about $5 each way IF you pay in Pesos). Or you could stay Downtown, at a real budget hotel like Hotel Plaza Cozumel, Hotel Mary Carmen, or Hotel La Casona Real (all at or below $40 US a night), Suites Bahia (about $45 a night, and includes breakfast buffet at Casa Mexicana), or Casa Mexicana (about $65-$70 a night, including breakfast buffet), and dive with any of several Dive Ops which either leave from Downtown or provide transportation to the Caleta, the marina from which the dive boats leave. Check out package prices at Aldora (as I said, a higher end Op, but definitely great service, and I understand that it will give a discount for cash), Tres Pelicanos, Blue XTSea, Living Underwater, and others.