I don't think you will get direct Heraklion from up here in the north during winter. A bit of internet searching suggests that you will have to go via Athens, although I'm sure other interchanges are available.
My advice to you would be make sure your accommodation has heating. We had a rather cold holiday in Crete in early May one year, and used the shower and getting into bed to get warm.
Keep an eye on the webcam. Some days it is achingly beautiful, but today the weather looks dramatic, so long as you are impervious to rain and wind.
Good luck with the planning, and let us know what you decide. I'd like to know how Plakias celebrates Christmas-time.
Arnaki