Traveling from Rome to Sicily

Define "best".

I think the best way to get around Italy is by private helicopter (even the Pope agrees), but only if someone else is paying. "Best" might be fastest, cheapest, most scenic, most comfortable, or the way that has the best gelato.

I'd probably fly, but if I had more time than money, a boat trip might be nice...

4 nights in Sicily does not allow you to see much. By all means fly and content yourself with one area of the island. BUT betted to spend those 4 nights somewhere less daunting and easy to get to by train, especially if you have to return to Rome to fly home.

I always recommend at least 2 weeks in Sicily, and that's if you're going to rent a car so you can move around more efficiently. Four days says "Palermo" or "Siracusa and Baroque towns" to me. The closest airport to Siracusa is in Catania (the busiest airport on the island). But I wouldn't do it. There are lots of great places on the mainland you could visit without adding at least one extra day of airports to your trip.

I would concur with acraven’s advice. Our first visit to Sicily was for 10 nights. We were based in Eastern Sicily following a Southern Italy tour. It started in Taormina>Ortigia>day trip to Noto, Ragusa, Modica & last night in Catania. Our favorite town was Ortigia. We knew we would go back. This fall we will spend almost a month in Sicily starting in Palermo. We will fly there from Rome, home out of Catania.