Ilias has a great location very central in Heraklion. They have a very hospitable, clean and convenient apartment equipped with proper cooking equipment. The restaurants within a stone's throw are top class, too. Must try Siga Siga and Peskasi downstairs!
Fair warning though, parking is rather difficult. We had to settle for parking at the sea port about 10 mins walk away and paid 3 euros per night. The parking there is fairly convenient since they're open 24 hours.