We only stayed in Heraklion one night - this is the largest city and is where the airport is that we flew into. We barely saw any of it because most of our time was spent Westward, however I think it's worth checking out.
Infinity City Boutique Hotel - lovely rooms, really nice breakfast, friendly staff
THINK TANK cafe - good coffee, beautiful rooftop seating area with lots of greenery
Plánē - cute restaurant with outdoor seating, right next to the hotel
Wine and cheese from small markets
Walking around the harbor
Old town had a lot of cute looking restaurants that we would have loved to try!