From the Messina Maritima RR Station (I assume near the port but do not know for sure) you can reach Taormina-Giardini in about an hour. From the rail station you'd take a bus (pretty frequent) up to the town, which is intensely touristy but really lovely and in a spectacular setting. I think any cruise guide would say that's your top day-trip destination from Messina since you have limited time available if not on a ship-sponsored bus trip. It's possible there is bus service from the port of Messina directly to the town of Taormina as well. A cruise forum might be a better source of info since not too many of us here take cruises.
Although I'm sure Taormina is nicer in the evening when the daytrippers have left, it's a smallish town and from the standpoint of sightseeing (as opposed to just relaxing), I think you can knock if off on your Messina day and won't need to return to it during your free time in Sicily. Sicily has a wide variety of sights scattered all over the place.
If for some reason you don't want to target Taormina on your day in Messina, you might consider Acireale. It was recommended to me while I was in Sicily, but I didn't have time to visit it. Online information suggests that it's an attractive Baroque town, not too large. It can be reached in as little as 76 minutes by train from Messina Maritima, but many of the trains take 1-1/2 or 2 hours.
There's a good chance there are non-cruise-related bus tours offered from Messina if you have a burning desire to see Mt. Etna.