Wheelchair access in Messina is generally good since the main attractions of the square and cathedral are both wheelchair friendly. If you are on a cruise to Messina then your walk to the central square should only take you around ten to fifteen minutes but be aware that there are some rough areas of the track. A pictured below, not all curbs are fully dropped and small tiling floor gives a slightly rough surface as you journey along the shopping central streets. It is also worth noting that there are some tram lines to cross and to avoid getting your wheelchair wheels stuck in these!
If you want a disabled Messina cruise tour then you can book excursions through your cruise company. However, there is not a lot to do and explore in Messina and I really would recommend exploring Messina on your own. If you want to explore wheelchair friendly Messina more in-depth then there is a hop-on hop-off bus and train that can take you to some of the higher churches and view points. This lets cruise passengers visiting Messina get a great aerial shot of the sea and the cruise ship they are travelling on. However, these hop-on hop-off services are fairly expensive and the main attractions in Messina really are the central square and cathedral which is based in this central square. The square has a beautiful fountain in the centre and paved flooring as pictured below. This is uneven and rough for a wheelchair user to travel across and there are very few dropped curbs to get onto this surface. Messina cruise port is famed for its astronomic clock which gives a really interesting twelve minute long display at 12pm (noon) where mechanical figures move around to music and chiming. This is the biggest mechanical clock in Italy and was a gift to the people following their bad luck in having a large earthquake. You can climb this bell tower for 4 euros for adults and 2 euros for under 18s when you enter the cathedral but there are a lot of steps so this is not recommended for those with a mobility impairment. This is a great wheelchair friendly activity in Sicily! 
The cathedral is in the central square and has ramped access if you follow the pathway down the left-hand side as you face the front of the clock tower. Once inside the flooring is marble paving slabs and is very smooth and level. There are beautiful decorations all around the cathedral to view and the wheelchair access in Messina cathedral is brilliant throughout the building. It’s a great place to take lots of stunning architectural photos. 
If you are thinking of visiting Taormina and Mount Etna from Messina port then I would really exercise caution if you are a wheelchair user of use a stick or walking aid. You can book very expensive disabled tours to Taormina and Mount Etna through your cruise company but once you get there many of the attractions aren’t wheelchair accessible! You can often book a private driver cheaper than booking through your cruise company, especially if you can gather a group together. if you do plan on visiting Taormina and Mount Etna with a wheelchair then I would recommend a drive to Taormina’s Porta Catania and a walk down Taormina’s level Corso Umberto which is the main pedestrianised shopping area. Food is expensive here, especially if you want a sea view but views are lovely from Piazza IX Aprile.
