I would use Moto Plakias, local family run company with about 50 cars very easy to deal with, Harris the owner will arrange for the car to be at either airport with the keys at one of the car booths very importantly these are open 24 hrs he will ask for your details by email so no hassle at the airport filling in papers, once you get to plakias just visit his office the next day to take the papers you will need.
Prices are about the same as everywhere else but you know that you will not be asked to pay a trumped up charge for minor scratches and damage that some car hire firms do although the damage was already there.
And we had some friends coming to Plakias and the plane was delayed 2 hrs so didn't arrive until 11pm this meant the car hire office was closed although they rang them before to explain the situation they just said there was nothing they could do and they would have to get a taxi into Chania find a hotel for the night and pick up the car the net day, so I went and picked them up brought them to Plakias and hire a car from Harris the next day.
Its also good to support local companies.
His email is maplakia@otenet.gr