Family Guy would definitely go R. There's no question about that, and the DVD version will be even deeper than that. The movie simply wouldn't work as a PG-13 movie... Though I'd tend to think the Studio would almost force a PG-13 upon them, because Teenagers are their biggest audience. But Seth has enough pull to make it R.
South Park, unlike these Fox Animation Domination shows have had the luxury of having a movie very early on. There's a lot of work behind a weekly series, and that's a big reason why it took the Simpsons 20 years to get a movie (Seth actually pointed that out somewhere, and said that's the reason why there hasn't been a movie yet). Of course, rumor has it that Imagination Land was supposed to get a theatrical release (I'm sure they'd have to clear all the cartoon likenesses possible, though). And yet another rumor stated that the Camp Krusty episode of the Simpsons was their idea for the first movie.