Ferries are a genuine alternative to Eurotunnel for crossing the Channel into France, running routes like Dover–Calais alongside longer options from other parts of the UK and Ireland. Pet policy is set operator by operator rather than standardised across the industry, so it's worth checking the specific company's current rules directly before booking rather than assuming they all work the same way.
On the shorter Channel crossings, pets typically stay in the vehicle for the duration of the trip, similar to Le Shuttle. For travel within France itself, the mainland-to-Corsica ferries are a notable domestic route that regularly carries pets — Corsica Ferries, for instance, prices a dog's passage separately from a small animal travelling in a bag, with pet-friendly cabins available at an extra cost on the overnight sailings, while Corsica Linea and La Méridionale offer dedicated onboard kennels instead.
Whichever operator or route you choose, the pet travel documentation requirement is the same as for any other route into or within France: microchip, rabies vaccination, and a valid EU pet passport or health certificate, checked against the specific crossing you've booked.