Omsk – Salekhard 2783 km, 6 days. Currently as of 2018. River boat. I don't know if it takes cars.
Some sea or ocean crossings that are longer than 1000 km, as the crow flies (current as of 2012):
- Travemünde–Helsinki: 1095 km
- Cadiz–La Palma: 1382 km
- Hirsthals–Seyðisfjörður: 1504 km
- Alaska Marine Highway has some long routes: Selgovia–Dutch Harbor (1096 km), Bellingham–Skagway (1451 km). But nothing ocean-going beats Bellingham–Homer with 2219 km. Question is if this is still a ferry considering it doesn't go very often (apparently just three times a year).
- Norwegian Hurtigruten takes cars: Bergen–Kirkenes which is 1541 km as the crow flies, but at least twice as long with the route it actually takes.
Even longer: The riverboatriver boat from Omsk to Salekhard (Siberia, Russia) runs for 2783 km. If I'm reading the timetable correctly, the journey takes 6 days (and a connecting ferry from Salekhard to Antipayuta is another 2 nights and 715 km). I don't think it takes cars, but I'm not entirely sure about that, as the only other way for people in some communities along the river to bring a car would be by winter road, so maybe there is a provision for that.
There may be other very long river boat journeys in Russia as well, in particular in Siberia. Siberia is big. Really big. You just won't believe how vastly, hugely, mind-bogglingly big it is. I mean, you may think it's a long way down the road to the chemist, but that's just peanuts to Siberia¹.
¹After Douglas Adams.