Based on Peters fights with the Giant Chicken I'd have to say peter. He takes some crazy abuse and keeps on coming. Homer does have that extra thick skull, but doesn't really have the needed fighthing ability.
OR, the Giant Chicken comes in and saves Peter, because who would the Giant Chicken have random violent sequences if Peter lost? Homer's got no initiative, and would rather lie down and play dead than fight.
Actually, in some recent eps, Homer has been doing some amazing stuff. In a play on Mr. And Ms. Smith, he had some pretty awesome fighting skills, and when he and Flanders started bounty hunting, he was shown to be very efficient. Homer might take it.
Having said that, they're both pretty much indestructible. Homer has some protective layer in his head, and as the black doctor of Springfield said, 'I could beat him over the head all day with this two-by-four and nothing would happen'. Peter has bleed more on screen, but he's also taken shit that would kill even the toughest of guys.
So it'd probably be a stalemate.
__________________ RUN RABBIT RUN
STRIKE OUT BOYS, FOR THE HILLS
I CAN FIND THAT HOLE IN THE WALL
AND I KNOW THAT THEY NEVER WILL
__________________
Right! Now, I'm on a mission!...If I can just remember...What?! I've got no time to talk - I'M ON A MISSION! And...what planet am I on again??
Gender: Male Location: Inner Workings of the Nth dimension
Both duke it out until hunger sets in, then they call a truce to get a bite to eat.
On the way to get some grub, however, they get into an argument about where to eat. Homer wants Krusty's, Peter for whatever reason is craving Italian. The fight reumes...
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Signature by starlock. Honorable mention to Marvelknight.