I haven't read Jimmy Corrigan, but a quick google, wiki and amazon preview doesn't really show me what McFarlane stole.
I mean, I figured I'd see something here or here, but no dice. About the only relation I found was a single thread on a forum claiming the same, but the only evidence they provided was a shot of the Stewie character and Jimmy both having football shaped heads.
I mean, from what I can tell, they're not even remotely similar in tone, character or approach. Jimmy Corrigan has more in common with "Hey, Arnold", from what I can tell. Is there more to it than that?