1) The old town.
Along the side of the Nerandzes mosque you'll find the street Odhos Vernadou: charming & lively at night. Places are set amongst crumbling venetian facades with candles in the walls. Opposite the mosque is a Turkish-themed place, 'Asikiko' - menu is in Greek only: their mezedhes & 'meat/fish in foil' dishes are excellent . Place was getting busier & busier when we left at 1am . (Take a look inside even if you don't eat .)
Next door is a reasonably priced restaurant aimed at tourists: 'Minares'. Next to that is 'Morphes' : good food & mainly a young Greek clientele. Next to that 'Bar Figaro' -good music & an imaginative interior : huge lamps and a giant tree.
There are many pretty courtyard restaurants . 'To Pigardi' 31 Xanthoudidou, has been highly recommended. 'Taverna Garden Ftochiko' in Souliou is romantic in setting, hearty in portions.
'Kyria Maria' , in the alley called Mohovitou that runs from the Rimondi foundation, has great food + is cheap and friendly. Just along from it : 'Vasiliko' right by the fountain is a friendly cafe with good coffee.
2) Area above the old harbour leading to Ideon hotel (Platia Pastira) . Sit and watch the sunset with ferry departing! A young Greek area. Try some of the town's fresh fruit juices. ..Follow the sound of the rattling frappe straws...
3) Inner (old) harbour ...! Crete isn't normally a place where you get hassled but you will here. Unless you are loaded, practice some polite refusals in Greek. I've actually seen tourists getting physically pulled towards a chair here . 'Knossos ', however, seemed reasonably priced & not too pushy.
4) Area by Porta Guora,: good food shops for picnics. In some of the side streets that run off Ethnikis Andistatis you'll find a number of old fashioned Kafenions and tavernas: try exploring here. Further on round: 'O Psaras' , by a church at top of Koronaiou is recommended.
5) The beach front/new harbour - I haven't eaten here. Samaria is said to be good. Here, the beach and food places stretch for miles!