We want to stay in Taormina and then take the ferry to Malta. Read we can fly into Catania and then take a taxi to Taormina spend a few days then catch a ferry to Malta. Can anyone help? Also is the ferry ride long and how rough are the seas. We are traveling early June 2017.

Do not think the ferry goes from Taormina.
I believe it departs from Catania.

No no big port in Taormina but no doubt Catania.

http://www.directferries.co.uk/ferri...y_to_malta.htm

There are frequent buses between Catania airport and Taormina.
The Malta ferry (catamaran) leaves from Pozzallo. The company offers car transfers from Catania.
http://www.virtuferries.com/?page_id=1539
Otherwise you can reach Pozzallo by train from Taormina via Catania - Siracusa (takes much more time, ferry pier far away from the railway station).

Flights from Catania to Malta are usually cheaper and more convenient.