I havent stayed at either but I can definately recommend the one I did stay at, Lambrinos studios. Also when you say 'hotels' are you sure that they are hotels? In Masouri its all apartments from what I remember.
Mopeds are pretty much essential especially if you are staying 3 weeks. You will want to visit many cliffs around the island and you will prob want to go to the supermarket or for dinner in Pothia which is a fair distance away from Masouri where you will be staying.
Have fun