Take a look at their policies on the things you might not be thinking about--interdisciplinary work (would he like to combine history/bio stuff? which school is more open to that?), off-campus study (which has more programs? is financial aid portable into off-campus study?), extra curriculars. Our impression of Colgate is that they tend to be more "by the book"--they have a way that they do things and that's that, whereas Kenyon has a long tradition of flexibility. Greek life, by the way, is more more entrenched and traditional at Colgate than Kenyon--at Kenyon, the Greeks are in the main south end buildings, with independents sharing the same buildings. Colgate has traditional Greek houses, down at the bottom of the hill in their own semi-off-campus world. That Colgate science building is sure gorgeous, though!
But I hear Kenyon has some new facilities! How does your son feel about climbing the Colgate hill all winter?