I went there a long time (20 years) ago, but I doubt it’s changed that much. It was October, the weather was fine – not too hot, and cool in the morning. Flew to Heraklion then got a bus to Chania via Rethimnon. Stayed briefly in Chania. It’s old and quaint and probably the most interesting of the bigger towns. Then we got a bus south over the mountains to Sougia, which was really nice. It was just a local bus – I remember the conductor offered us chestnuts out of a massive sack that was part of the cargo. There may have been live chickens on the bus or I may be over-romanticising.
From Sougia we got a bus to Ormalos and walked down the Samaria gorge. Even in October it was busy. We ended up in Agia Roumeli and got a boat back to Sougia then off to Palaiochora where we hired a car and went off to Elaffonissi beach (deserted and spectacular).
At some other point we went to Loutro (by boat, there’s no road). Then off via Rethimnon to Heraklion.
We just turned up at each place and found somewhere to stay for a few days then moved on. It’s not high season. If I did it again I’d probably do some more proper walking as there are lots of long distance paths. As it was we did some local wandering.