Both are quite decent hotels.
After you finalise your itinerary I would use the points at the hotel where the rates are highest for the days I want to stay if its case of either or then I would stay at the Hilton Prague especially if you are likely to get lounge access.. the lounge IMHO is one of Hiltons best in Europe.
mike
After seing CHG's post its rare that two Ftakers agree on just about any topic