Don't spend the money on a tour. You can take the tram to the top of the rock on your own easily. Don't miss the siege tunnels - they were great! Tour guide misjudged time and we missed the museum because it closed at 4:00. We were supposed to be refunded but that never happened.
Wow! What a port! We were lucky because they had a yacht show at the time. It was unbelievable! This is truly a beautiful port! Easy to get around - walked everywhere. Tried to book a private tour but they were very expensive. Found it was easier to just rent a car and drive if you want to explore outside of town. Trains work too.
Port is very industrial and very far from Rome (at least 1 to 1 1/2 hours). Rome is another must-see city though so well worth the ride! Easy to do on your own and to walk or take a city sight-seeing bus, but you will need to book a tour for the Vatican and would also suggest a tour for the Roman Forum/Palatine/Colosseum (one ticket gets you into all 3).