Alexander Vandegrift, hands down, with everyone else being an also-ran. Roy Geiger gets an honorable mention.
I think Vandegrift is most likely to be given the over all title of "Best Marine CO". Chesty Puller is the man and the Marines Marine but he was relatively low ranking.
I'm going to go out on a limb here and say anyone who wore the Eagle, Globe and Anchor. The Marines were blessed with great Jr. Officer's and Jr. Field Grade Officers. Moreover, they had the best NCO's of any branch.