Hi,
The easiest way to get from the Marco Polo airport to your cruise ship would probably be purchase the transfers from the ship line. There is a special waterbus service that runs from the airport to the city, about 10 euros a person, but it does NOT go to the commercial port area. The regular city waterbus service also does NOT go into the actual commercial port area. You can also get a land taxi that can take you from the airport to the port area. I don't know what the charges would be for this. There are also water taxis that can take you from the airport directly to the port but these run from 60 to 80 euros. There is also shared bus transportation that goes from the airport to the Piazzo Roma and the railroad station area which looks close to the port but would be an extremely long walk trying to drag along all your luggage.
Have a great cruise.
