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Peter took the MacArthur Genius test or whatever test that was and his test score said he was retarded. That would put his IQ in the range of 55-69. In the episode where Homer had a crayon removed from his brain, it increased his IQ by 50 points to 100, so Homer's IQ is exactly 50.

Conclusion: Peter is smarter than Homer. Well, at least in terms of IQ level. This depends on whatever criteria you're using.