I was just recently revisiting old episodes of the harmontown podcast, and there's one near the start where Dan Harmon rants about how Good Will Hunting is not a good movie. He particularly thinks the "how do you like them apples" scene is dumb. So I'm guessing, since Harmon wrote that speech, that Jeff Winger shares his opinion. He also mentioned the theory that William Goldman actually wrote the screenplay, but I think the main thing is that he thinks it sucks.

I believe it was the tour episode when they're in Massachusetts.