You will see here that on Friday, April 3 Lane Lines has a Friday evening departure from Piraeus to Rethymno at 7pm, arriving on Crete at 7:30 the next morning.
If you do opt to fly to Heraklion there is a bus to Rethymon. You can see the schedule here:
Hellenic Seaways also offers a highspeed ferry to Rethymno from Piraeus but this year's schedule isn't available yet. Last year this service began on March 21, so it's possible you'll be able to take that one instead if they offer it again.
When they do you'll be able to see it and book it below, although at that time of year advance booking is unnecessary: