Three of us went out in November a few years ago. We all agreed it was well worth the effort.
We travelled Heathrow to Athens with BA, then got an internal flight to Heraklion. A very smooth trip, not too expensive, and a very interesting stop-over in Athens. We picked up a hire car at the airport, which we used most days to explore the area. It really is fantastic off-season.
We stayed at Kostas - arranged in advance by email. Other places are available these days to I think. I hope another board member might be able to offer suggestions.
Although quiet, we managed to eat and shop with no problem. Sifis stays open, and was quite busy some nights. I believe more places are open these days.
Ostraco (downstairs) was open, and very warm on the chilly evenings.
It was great to see the bay without sunbeds - and it was still warm by day. I swam most days, the sea was warm, if a little choppy sometimes.
I would say - give it a try!