Getting from Messina to Palermo

There are through trains from the mainland to Palermo. They get ferried across, and you don't have to deal with getting from a train to a ferry terminal and vice versa. Also, it is quite the experience. That is what I would do.
I am assuming that you are stopping over between Venice and Sicily? Otherwise... It is quite the train journey!

I took the train from Messina to Palermo - no problems. There are multiple direct trains a day and the central train station is next to the port. The direct train takes about three hours. I actually divided my journey to Palermo in two stops. If you have any extra days or interest, the scenic views from the Sanctuary of the Black Madonna at Tindari are gorgeous and there is an archeological site with Greek ruins right there. To get there we took train from Messina to Oliveri, stayed one night there at a BnB and the owner drove us up to Tindari and picked us up several hours later. We then caught an afternoon train to Cefalú and stayed there two nights. If your tour does not include Cefalù it is well worth a visit on route to Palermo or as an easy daytrip from Palermo.

If you prefer bus travel, the bus station is very close to the Messina train station.

traveling by train from Venice, then by ferry to Messina.

Are you planning to stop along the journey, or do you plan to travel all day to reach your destination?

It’s a very L-O-N-G train journey (15,5 - 21 hours) involving at least one (maybe 2) train changes from Venice to Palermo.

Have you considered flying?
You may check flights here: skyscanner.com