I second the train. Timewise for flights, you have to factor in the time to get to and from the airports and to arrive at the airport far enough in advance.

Check out both Trenitalia and Italo, pick a time that you like, and reserve as far in advance as you can, for the lowest fare. Incidentally, in second class at least (the only one I know about, being a plebian), seating layouts differ between Trenitalia (facing across tables) and Italo (airplane-style rows). The wonderful Man in Seat 61 has lots of information at https://www.seat61.com/train-travel-in-italy.htm.