Pergeri Apartments is in a great location- close to a bus stop to Oia or Fira and a about half an hour walk to Imerovigli and Skaros Rock.
If you don't like the idea of staying somewhere where people walk past your hotel all the time, an affordable place where you can watch the sunrise from the balcony, this is the place for you. It is also close to the walk from Fira to Oia (Although you would join the track in Imerovigli) and is a much quieter area than Fira or Oia which I enjoyed.
The hosts are lovely and sweet, and I felt very looked after. They even cleaned every day which I did not expect and you can order a simple but tasty breakfast to eat on the balcony. You can open the doors to get a lovely breeze through the apartment too.
The only thing I would caution is that the mattress is quite firm so if you have back issues it may not work for you.