Be careful in Naples pickpockets bag snatchers and muggers are a big big problem the place is dirty graffiti covered city i suggest that you catch the fast ferry to Capri the ferry is is on the left next to where you dock a much nicer place to se.
It is easy to DIY if you do enough research. Go to cruise critic and their ports of call section for tons of info.
Villefranche: you are right in town
Naples: you are right in town
Pisa: You dock in Livorno and have to get a bus out of the huge port complex. From town catch the '1' bus to the station and from there the trains run frequently to Pisa, and take 15 mins.
Villefranche is a wonderful place and you dock in the bay, tender to shore. You also have easy acccess to Nice and Monaco, Monte Carlo from Villefranche- there is a train line and I believe buses to both these places. You can walk from Monaco to Monte Carl.
We always DIY these ports by train. From Villefranche you can easily get to Monacao/Monte Carlo, Nice and Cannes. To save valuable time check out the timetables on www.voyages-sncf.com (scroll to the bottom of the page and click on the union jack for the English version)
From Naples you can catch the Circumvesuviana train to Pompeii, Herculaneum or Sorrento. Check out http://www.sorrentoinfo.com/timetable/local_train_sorrento.htm. Alternatively, you can catch the hydrofoil to Sorrento, Capri or Ischia These are frequent and fast - if you need timetables, post again and I'll dig them out
From Livorno, you can travel to Floence, Pisa and Lucca by train. We usually get the ship shuttle to downtown, then the no.1 bus to the station (tickets on sale at the newsagent shop across the road) Check out http://www.trenitalia.com/en/orari_biglietti/index.html for timetables