Nice, clean and comfortable (airconditioned nicely) apartment near the town center, just behind the Venetian walls. Only a 10 minute walk to the main shopping area and museums. The perfect base for all sorts of trips and visites. (be sure to check the park/open air theatre around the corner)
We loved staying in the city for a couple of day's during our three weeks holiday. Heraklion is worth a visite, even though most Cretans escape the town during the summer. (At least, that's what they say, but luckily, there were more Cretans in town than tourists ;-)
Great places to eat, just as long you avoid the tourist-trap-restaurants with pictures of the food displayed.