In asking for the BEST dive op or BEST lodging on Cozumel, you will get a long list of "BESTS" . It will be a running list of dive ops and/or lodgings that will ultimately turn into a pep rally.
In General, there are MANY dive ops who offer small fast 6 pack boats as well as larger boats. There are boutique style dive ops and those who offer bare bones service, both of which are wonderful depending on what a diver is looking for. The same goes for the lodgings as there are small hotels or B & B's, in town, out of town, AI or non-AI.
Therefore, in choosing a dive op and lodging, of course take the list of responses under some consideration , but, if you have not done so already, I highly recommend you take a look at the TRIP REVIEWS from the past few months, not necessarily the "MY BEST" lists. Then choose 3 -5 dive ops and accommodations that are of interest to you. From this list you may have questions that can be answered here on the board or contact the dive op/hotel directly. Once you have your best, then all you have to do is make the reservation, plan, pack and GO !!!
Overall, there are several dive ops that meet your requirements of 2 adults, advanced divers ( 100 dives) , 40+ age. looking for small group to dive with, no crowds, willing to pay extra for best dive sites off the beaten path. . Perhaps focus on a boutique dive op, six pack boat. Also, lodgings that are way south or way north can be, for some folks, inconvenient as the cab fare can become expensive if you want to take in the sites, activities, and restaurants in town. If staying a distance away then a car rental may become an option, however, do consider the cost of the car and full insurance which can make a rental pricey. AI's are available, but, definitely research for the quality of food.
Regardless of what you decide upon, here's to wishing you a wonderful dive trip. Also, please do post a trip review. Not only is it so neat to read about the fantastic experiences of fellow divers, but the information that is shared really does help out others who are looking for their next diving vacation experience !