PG says that the comment quality is the most worrying part of the site ("Bad comments seem to be a harder problem than bad submissions. ")

Perhaps a better way of measuring the difference, would be to parse the comment threads and compare length (PG: length of a comment is directly proportional to the intelligence/civility of the poster) or frequency of memes.

I suspect this would show HN to consistently score higher, but not as dramatically as your analysis of posts.