Fast answer
For a first Polignano stay, choose the old-town cliff core only when the sea-facing setting is the point of the overnight and you are willing to check room access, stairs, bags, and crowd pressure. Choose a sea-view terrace when the room experience is the trip's emotional center, the station side when arrival friction matters more than atmosphere, and San Vito or the north coast when the stay needs more coast space. If the trip needs several nights of beaches, dinners, and onward movement, compare Monopoli before booking Polignano.
If you only do one thing
Default to a short old-town cliff stay when Polignano is the highlight itself. Default to Monopoli when the coast base needs to work harder across multiple nights, then visit Polignano for the cove, viewpoints, and compact evening after checking trains and sea conditions.