The Island Ferry leaves town (going North) on the odd hours and leaves from the north going south on the even hours. Not sure exactly what time it leaves Costa Maya (probably a little before the hour). This is up to 6 pm when there are boats both North and South at 6, 7,8, 9, and 10. Then on Tuesday, Wednesday and Saturday there are runs North at midnight and 2 am provided there are four people to go on the boat.
Hope this helps.