Save money and time booking your own tours of Crete before you start your trip.
Maybe a visit to a former leper colony isn't everyone's idea of a great day out, but the locale is so beautiful and the abandoned buildings so evocative that you'll come away enchanted if a bit melancholy. It will also give you a chance to do some mermaid-searching, as this lagoon is said to have been a haunt of Britomartis, a Minoan mermaid goddess.
Crete is such a big island it starts to feel like the mainland - but you can leave it all behind and go explore a much smaller island just off the coast and visit "Europe's Southernmost City" Ierapetra at the same time. This is an especially nice getaway if you're staying along the North coast of Crete, which can get a bit crowded. The Southern coast is much less built up, and can give you a sense of really getting away from it all on this day-long tour.
If you visit Crete, the palace of Knossos is mandatory. It's fascinating, disturbing, and edifying all at the same time. The Archaeological Museum is compelling. While the full museum may not be open at your visit, the smaller temporary exhibit is filled with such choice objects, you won't mind.
This very full day tour - 16 hours - takes participants to the top of the Samaria Gorge, where they then walk to the bottom. It's not for everyone, but the reasonably fit will have no trouble with it. And if you do have trouble, there are evacuation donkeys. But do read my article on the Samaria Gorge so you're well prepared for this beautiful yet rugged area.
This full-day tour includes the historic monastery of Arkadi, Rethymnon, and Chania. It's an easy way to explore the western portion of Crete.