Isla Mujeres [1]’s western side has calm water and extensive coral reefs that make for excellent snorkeling, though relatively few spots are accessible from the shore. Snorkeling tours can be booked om Playa Norte [2] and at the ferry pier (or at your hotel) and typically cost US$20–30 per person for 1.5–2 hours.
Most groups go to El Faro (The Lighthouse, near the ferry piers) and Manchones (near the southern end of the island), where the coral and sealife are in relatively good shape despite the heavy traffic; if possible, go in the afternoon to avoid the crowds. Dive shops also offer snorkel trips and are more apt to take you to less-visited areas.
Another option is to take a trip to Isla Contoy [3] (US$65, including the US$5 park entrance fee), which includes snorkeling on Ixlanche reef in addition to exploring the island. Boats depart Isla Mujeres around 9:15 a.m. and return at 4 p.m.
You can snorkel on your own at Garrafón de Castilla Hotel and Beach Club (Carr. Punta Sur Km. 6, tel. 998/877-0107, 9 a.m.–5 p.m. daily, US$3.50), at the southern tip of the island. The club itself is pretty desultory, but you can explore over 300 meters (894 feet) of coral reef, including the part used by its much-hyped neighbor, Parque Garrafón [4].
Snorkel gear rents for US$5, and lockers and towels can be rented for US$2–2.50. Hour-long tours to nearby Manchones reef can also be arranged (US$20–25 pp, including equipment).
Links:
[1] http://www.moon.com/destinations/cancun-the-yucatan/cancun-cozumel-and-the-riviera-maya/cancun/isla-mujeres
[2] http://www.moon.com/destinations/cancun-the-yucatan/cancun-cozumel-and-the-riviera-maya/cancun/isla-mujeres/sights/playa-norte
[3] http://www.moon.com/destinations/cancun-the-yucatan/cancun-cozumel-and-the-riviera-maya/cancun/isla-mujeres/sights/isla-contoy
[4] http://www.moon.com/destinations/cancun-the-yucatan/cancun-cozumel-and-the-riviera-maya/cancun/isla-mujeres/sports-and-recreation/parque-garrafon-ec