Maybe not exactly the same situation as yours, as we weren’t joining a tour and we went from Rome to Palermo, not from Naples, but the flight was really quick and convenient. We rented a car at the airport and headed west, not into Palermo, so that may be another difference.
Unless you’re getting a good night’s sleep on the ferry (which will likely be stable and not jarring, but can you get a private sleeping berth?), taking the plane’s the way to go. We finished our driving on Sicily and took a car ferry back to the toe of the mainland of “The Boot,” driving to the Amalfi coast from there.
Unless a train or ferry is much cheaper or allows you to travel while you sleep, cutting out one night of lodging, fly and get to Sicily sooner. Or stick around the mainland for an extra day or two, and then fly just in time to start the Sicily tour. Have a good trip(s)!