Decent car rental service offered by Sixt in Heraklion.
The airport office is fairly accessible, with multiple counters being available for signing contracts. However, the line there was of about 10 people and we had to wait for close to 1 hour. What was even more frustrating was that it didn’t make any difference that we had already booked AND paid for our reservation online.
The parking lot is the farthest of all, but overall it’s not more than a 5-7 minute walk from the arrivals terminal.
You can leave the car at any time, if it’s too early/late you can use the secure key box at the airport office to leave the key.