If you want to see the Vatican and the Colosseum on the same day definitely take the ship's excursion. You will have a guide that not only will explain everything, but will get your tickets and you won't have to wait in line. Rome is always very crowded, not only with cruise passengers but with tourists from all over the world.
The first 2 times we went to Rome we took ship's tours.The guides were excellent and we were very satisfied with the tours. They are expensive but worth it. Now when we go to Rome we do walking tours on our own. Have a wonderful cruise.