If you want a completely untouristy island you should go to Chios. It has real Greek island life and not a package tourist for hundreds of miles. It has lots of decent scenery, great cafe culture in the main town, decent connections back to Athens and to Turkey, and decent food.
In Crete, I'd recommend Heraklion. It's a beautiful old town, with a Venetian harbor, lots of old buildings, and good food. The archaeological site of Knossus (one of the centers of the Minoan civilization) is nearby, too. The beach there isn't great, though.
I have been to the Greek Island of Skiathos. Its a small relatively unspoilt Island which has some beautiful beaches and countryside to explore. Skiathos town itself is very attractive. I stayed in Koukounaries which is lovely and I highly recommend.