The port is actually a few miles away, at Pireaus. Transportation is available and Athens is a great historic city. We did not take a ship's tour but used a driver with an independent group. Worked great, we saw all the major sights and even had time for some small purchases.
Naples as a destination is not a favored city. It is dirty and covered in grafitti. However, it is the gateway to Pompeii, Herculaneum, and the Amalfi Coast...all of which are very worth visiting. For the Amalfi Coast we booked an independent tour. It was every bit as lovely as we expected, and a true highlight was a lunch in Ravello at Cumpa Cosimo Restaurant. Our driver knew the restaurant called to be sure they were open, and the owner greeted us warmly and offered a delicious home made lunch.
Good tour, interesting sites. However, there was disagreement between the group leader and the tour guide about the obligatory stop at the carpet weaving school which created an awkward situation. The tour company should have made the stop known in advance.