Hi Poppi,
I’ve done that connection before! The easiest option is definitely to fly—several low-cost airlines like Ryanair and Air Malta run direct flights from Catania or Palermo to Malta, and it’s only about an hour in the air. The ferry is possible too, but it runs from Pozzallo (about 1.5–2 hrs south of Catania by bus), so it adds some extra travel time. The fast ferry takes roughly 1 hr 45 min and can be a fun option if you don’t mind the transfer.
If you’re short on time, I’d go with a flight. If you want the experience of arriving by sea and don’t mind a longer journey, the ferry is a nice alternative.