"Best" reef (or cenote) is going to be highly subjective, and the shop is generally going to take the boat to whatever site they want anyway, based on numerous factors (sometimes diver preference is one of them, but there are others, both pragmatic and self-motivated).
Being comfortable and having good buoyancy skills are considerably more important in a cave/cavern environment than they are in the open ocean, so unless you're sure you are good-to-go, it might be best to get re-oriented with an ocean dive before doing a cenote dive.
As for cenote dives, if there's an option, I'd try to check out Dos Ojos, if they do the dive from down in the Bat Cave (just being in there is an experience in itself !)
Car Wash is another good one, that i recall being very entry-freindly. But, you may not find a group going to either of these, and just like with the boat dives, you may have to go with the flow (which ain't a big deal, it'll be amazing no matter where they take you. And if the ocean conditions are really gnarly, hell, I do nothing but cenote dives !!)
