There is a daily ferry from Pireaus Athens, which arrives early in the morning. Most of the boats arrive in either Chania or Heraklion. Ferry tickets may be acquired through minoan lines or anek lines. (http://www.anek.gr/englis...)
There are regular bus services from both Chania and Heraklion. All busses stop at the bus station, just west of the center of Rethimno. From the bus station it's a 15-minute walk or a 5-minute taxi-ride to the ferry.
By plane
The distance from Heraklion to Rethymno is 80 km and from Chania to Rethymno 56 km. Chania airport is much smaller and far less busy than Heraklion airport. Crete flight schedules.
By ship
Ferry services from Athens Piraeus port to Rethimno Crete island
By bus
You can get to Rethymno by regular bus lines from Chania or Heraklion both have an airport. The coaches are operated by two KTEL companies (http://bus-service-crete-...), (http://www.crete-buses.gr/). To get to Rethymno from Heraklion it takes approximately 90 minutes and costs slightly over 6 â¬.