The wife and I did a similar cruise in November 'last year. This is what we did :-
In Venice, we got a two day Venicecard. You can get them for different periods of time and they are great for the water-buses. We spent two days getting on and off to visit various places.
In Dubrovnic we WALKED to the old town!! It an hour at a slow stroll from the dock to the town. My wife thinks that taxis are at the dock but I cant remember. The walk around the walls is a MUST!
In Piraeus we walked to the station (very easy to find), took a train to Athens and walked up to the Accropolis and looked round all the ruins.
In Kusadasi we had pre-booked a private tour to Ephesus. This place is a MUST SEE! It really blew me away.
In Naples we took a ship's tour to Pompeii. I have to say that having seen the Accropolis and Ephesus and even the walls of the old town in Dubrovnic, I was disappointed. I think there is another site like Pompeii (Herculaneum??) but I can't comment on that.
I don't know how long you will have in Rome but it is very easy to travel around the city. We were in Civitavecchia for two days and traveled to Rome by train and took the underground (subway if you are american
) to the Colloseum. A short walk to the Forum was followed by a longer walk (aided by directions from two policemen) to the Trevi fountain and from there to the Spanish Steps, back onto the underground the the train station for Civitavecchia. That was day one. Day two was to have been to th Vatican City but we were both so tired and had had so much culture and had seen so many ruins and great sights that we decide to wait until we go again (we threw our coins in the Trevi fountain).
That's all I can tell you except to say that if you are confident in your ability to find the various places you want to see having first checked it out on the webyou wont take many ship's tours. Remember, almost everyone will speak English and we found them to be very friendly.
If you want any more info on the places we went to just ask and I'll do my best.