Sicily/Messina- Cruise ship

It appears from the title of your post that you will dock in Messina and want to go to Taormina -- correct me if my assumption is wrong. With regard to "...wondered if we should go with the cruise boat excursion or can we do our own?", please consider this. You can do it on your own and many will advise doing so. There isn't any doubt that doing it on your own will be less expensive than taking an excursion through the cruise line. We have cruised extensively and if we are just going to stay in the town where the ship docks we do things on our own. But if we want to do anything that involves traveling a good distance from the ship we take a ship excursion. If there is a delay returning to the ship and you are on a ship excursion, the ship will wait for you. Not so if you are off on your own. In many places on our Mediterranean cruises there have been delays returning due to bad traffic jams and other problems. We have seen, on several occasions, people literally running along the pier trying to get back as the ship was pulling away. Not trying to tell you what to do, just relating our experience.

If you go to Taormina itself the town is lovely and just strolling about is a joy. There is a very well preserved Roman theater there, and a trip to Mt. Etna is, in my opinion, not to be missed. Rick Steves has a guide book to Mediterranean cruise ports you might want to get or perhaps check out at the library.

I've never cruised, so I have no comment on the risk of making your own way to and from Taormina, but there are relatively frequent (very roughly hourly) trains from Messina Centrale to Taormina-Giardini. I would never, ever plan to return via the last train scheduled to get me to the ship on time. It appears that the distance is less than 35 miles, so I guess a taxi would not be a crazy back-up plan.

You can take a look at the schedule on the Deutsche Bahn website. To check fares and purchase tickets, go to the TrenItalia website. Fares are low.

Note that if you use the train, you'll first need to get to the main station in Messina (check Google Maps to see how far it is from your cruise-ship dock), then on the other end you'll need to take a bus up the hill to Taormina.

Thanks to both of you for your help! Do you think that Mount Aetna is a must see if we went to Pompeii the day before?

No. I think it's cool to see it in the distance (which you will, unless the weather is significantly overcast). You can take a little train that goes around Etna (don't remember whether it goes all the way around or not, but I'm guessing that it does). That takes more time; it still doesn't get you up to the top of the volcano, which means adding on a tour. It wasn't important enough to me to devote that much time to it, but obviously plenty of people take the opposite position.

Pompeii is an entirely different situation, because you have the ruins.

To answer your question about Mt. Etna and Pompeii, my answer is "Yes", you should try to see both if time allows. The are totally different. Etna is still active and the landscape, particularly near the top, is (for lack of another word) eerie. The ruins at Pompeii are the "end results" of the eruption of Vesuvius and shows what things were like before the eruption. Definitely think both are in order, but that's just my perspective.

Thanks so much for your help!!