In Mujeres, the three major choices have been listed:
Marina Paraiso or Milagro are a little closer to the action and more of a cruiser hangout (Milagro in particular). Puerto Isla Mujeres is a little more removed and more resort-based.
The anchorage is pretty nice too. Close dinghy
ride to shore, land on the sand beach, lock your dinghy
to a tree and walk to town. Or dinghy to Milagro / Paraiso for sundowners.