Ultramar Ferry is the main ferry which will transport you to Isla Mujeres or Cozumel depending on the port location. They provide very reliable service and I highly recommend you purchase your tickets online as e-tickets. The tickets online will be the cheapest you find anywhere. There are booths near each port location which sell Ultramar tickets, but they are agents working on commission, so their prices will be higher than what you pay online. Your tickets get scanned upon getting on the boat, so e-tickets work perfectly.
Your next alternative is the Xcaret Ferry to Cozumel from PDC and Tulum.
ADO is a bus system in Cancun that will take you to and from the airport and drop you off at stopping points near several hotels, including Downtown, Cancun.
ADO is a great form of transportation if you're on a budget and are looking for the cheapest option to get from point A to point B!