From the Athens port Piraeus several daily ferries go to Heraklion and to Chania. Usually the boats leave from Piraeus in the evening between 8pm and 9pm and arrive early in the morning around 5am or 6am at Crete.
Escpecially in autumn, but occasionally year-round when the winds are high, the ferries might be canceled because of a storm warning. Then it comes to delays, sometimes for several days. In severe weather please ask your ferry company or directly at the port, if the boat is actually operating.
There are numerous ferries from Italy and Albania which approach Corfu, Patras or Piraeus. To go further by boat to Crete, you always continue your journey from Piraeus (Athens).