There are 183 inhabited islands and I have been working my way through them for many years. Still a few to go yet. Have a look at the Greek islands page on this site.
As always, it depends upon what you want to do.
1. Peaceful, eating, drinking, walking, sitting by the harbour and watching:
Paxos, Symi, Alonnisos, Lesvos.
2. Beaches: Skiathos, Crete, . There are very few large beaches in Greece which is a mountain range created by Africa hitting Europe a year or two back when I was young.
3. Night life: Corfu, Crete, Samos.
4. Archaeology: Thassos, Crete, mainland.
Don't forget the mainland: Parga, Kavala, Delphi, Corinth etc.
The choice is enormous. I've never had a bad time yet.