The Aressana Hotel in Santorini is very nice. If you can, you may want to splurge for the honeymoon suite.
We stayed at the Petasos Town Hotel in Mykonos. Very nice, clean and quaint but you may want something more luxurious for a honeymoon. The good thing about that hotel is that they have a shuttle that takes you to the Petasos Beach Hotel (the sister hotel) and you get to use their facilities. The Petasos Beach Hotel is very expensive. It was cool b/c we spent under $200/night for the Petasos Town Hotel but got to use the other hotel's pool!
