The nature is everywhere and really superb, especially the contrast between sea and high mountains
The Minoan palaces: don't miss the fact that you are in the cradle of Europe. Knossos is not necessarily the best Minoan palace but certainly the most crowded
Heraklion Archaeological Museum has the best collection of Minoan art in the world. If you can go when it is quiet it is definitely worth a visit.
The Old Towns of Chania and Rethymnon with their mixture of Venetian and Turkish architecture