The hydrofoil is the most convenient choice for most travellers: it connects Trapani to Favignana in about 30-40 minutes and Marsala in around half an hour, with many crossings a day — up to about twenty in high season. It carries passengers and luggage only, not vehicles.
The ferry, run by Siremar and departing only from Trapani, is slower — about an hour — and less frequent, with just a few crossings a day. Its only advantage: it carries cars, scooters and motorbikes.
Our advice is simple: unless you have a particular need, take the hydrofoil and leave the car on the mainland. Favignana is small and flat, and bringing a car is almost always more of a burden than a benefit — we explain why further down.