We used BA to visit early in May, scheduled flight into Heraklion and booked a room at Skinos, just outside the village on the Souda road.
While it costs a little more than Olympic charge (and of course, no last minute deals!), the flexibility is great. This year we stayed in Plaka on the NE of the island to visit Spinalonga and Knossos, then drove down via Ierapetra to Plakias. The drive was enjoyable but too far for a day-trip from Plakias.