You can fly to Sicily from Malta but the coolest way to get there is by ferry. You can hop on the Virtu Ferry (which is a passenger/car ferry) and be there in less than 2 hrs. The ferry cost 73 euros per adult (roundtrip) but if you have kids, they travel free. The ferry to Sicily is cheaper on Sundays though.
The ferry isn't long but one day trip won't cut it. Best you take at least 2-3 days so you have enough time to visit Etna, the Ragusa, Modica and Donnafugata castle. Oh by the way, no tours take you to the top of Mt Etna to see the crater. Still, worth doing the trip though
I too agree you want to spend a few days there to soak it all in from the Greek temples of Agrigento to the Roman Mosaics at Piazza Armerina. There are also archaeological sites like Siracusa with Greek and Roman Theatres. don't forget trying Sicilian wine, cheeses and almond sweets and honey.