What is more common to say: The ship arrives in the harbour or port of Lisbon?
The words have different meanings.
A harbor refers to an area of water that is protected (by natural or manmade breakwaters) from the open ocean.
A port is a place where large vehicles load and offload and where people enter a country.
So the ship enters the harbor of Lisbon when it sails into the calm water; it enters the port when it actually docks.