A couple of years ago I was in Crete too, more for family summer vacation than photography. But I find the Heraklion harbor quite charming during summer evenings: nice long walk past the Venetian castle, both scenic and lots of interesting people (local couples and fisherman). I found it much less tourists than other major Greek Islands or Athens.
I did the usual touristic things around Crete, such as the Malia Beach, Zeus's cave, Knossos Palace, etc. But I find them not that photogenic.