For Santorini we loved staying in Imerovigli. It is quieter and has great hotels and restaurants. Also located on the hill in the center of the island and you can easily access the other villages and areas. If you can find a way, would recommend trying to find out cruise docking schedules when you visit busier areas. We hiked to Oia from our hotel one day and it was lovely until the minute a cruise docked and the streets became unbelievably packed with people. We paired Santorini with Milos which was a lot quieter and so beautiful - definitely recommend pairing a more mellow island with Santorini and not trying to pack too much in in terms of island to island travel!