Make sure your maps are current, some friends ran on a sandbar near Isla Mujueras last year as weather has a way of moving things around faster than buoys or maps can be changed.
You can get inside the reef at Isla Mujeres to sleep and rest up.
Tulum is probably the next stop inside the reef. If you are sailing you are going to need your engine between Isla Mujeres and off Cozumel, the current can be strong. I've clocked it some times at 9 mph.
There are other spots but depends on your draft. Behind the ATOLLs is the best place to get some sleep. Chinchorra and Turneffe.