I have been many years to Patmos, until I became a mother. We have stayed many times at captain's house. Cathy the owner is a very nice woman from the island. She is very sporty (she has told me that once she was a swimming champion of Greece) and you can find her every night at her bike at the boats waiting for new quests. The service is great. The view at the front perfect. At night you can hear the big ships coming in.
A long time ago I fell in love with the island and its inhabitants and I can think of no better place then staying in the captain's house.