Long term - Morehead City Yacht Basin by a long shot. Staff, location, beautiful docks, clean bathrooms, cheap laundry, pump out, fuel, walking distance to great restaurants, great area for paddleboarding from the boat, great contractors. Walking distance to a hardware/rigging store. No cons as far as I’m concerned.
Town Creek Marina is putting in all new docks, so that would be my second choice long term in that area. Not walking distance to town, but a short bike ride...great staff, boat yard onsite, pump out, fuel, onsite restaurant, ships store......paddleboarding here too...
Short term - any of the previously mentioned are good.
Beaufort Town Dock are transient only. Great spot for a few nights though!