There are a number of marinas you can check in at in Isla Mujeres, el Milagro, Paraiso, Puerto Isla Mujeres, Marina del Sol, etc. Call on 13 or 16 for a slip or anchor
out in the harbor and dingy in to the Port Captains dock
. There are 2 ferries running every 1/2 hour to Puerto Juarez (Cancun).