By air. Cozumel International Airport (CZM) sits a few kilometres north of San Miguel and handles direct flights from a dozen US cities, plus Mexico City, Cancún, and seasonal European charters. A taxi to town is about US$15; airport collectivos and hotel shuttles also run.
By ferry. Two competing ferry lines — Ultramar and Winjet — run roughly hourly between Playa del Carmen on the mainland and the San Miguel passenger pier. The crossing takes 45 minutes and costs around US$15–20 each way. It is straightforward, comfortable, and the best option if you are combining Cozumel with the Riviera Maya.
Car ferry from Calica (south of Playa del Carmen) takes vehicles to Cozumel four times a day. Cars are not strictly necessary on the island — taxis and scooter rentals are plentiful — and the rental will probably be cheaper in San Miguel than driving your own across.