Calling Pop "the greatest NBA coach of all-time" isn't such a bold statement on the surface, but it is when you consider how most players, along with antiquated/casual media and fans, usually judge such things.
James, like others who share this view, probably think this because he has 5 rings, without an all-time great perimeter player or dominant physical force like O'Neal. He probably thinks, "How many would he have with me, Jordan, Bryant, etc.?"
So really what this is, is the usual slap in the face to Duncan, the player, specifically and the big three in general. Sure, they wax on about Duncan's intangibles, but you can tell they think playing for Pop and his "system" (which was actually only his system for a few years and only looked they way it did because of the personnel), is most responsible for the 5 rings.