To me, the mark that separates the truly elite, "legendary" coaches is the ability to win two or more national titles, college or pro. I think the second title is the difference between a coach who may be legendary at his own program, his conference, or his region of the country vs. the coaches that are legendary on the national stage...the ones who can be measured against the great coaches of past era.
Since 2000, that leaves us with Coach Saban and Urban Meyer at the college level, and with Bill Belichick and Tom Coughlin at the pro level.
You have other guys like Bill Cowher who is certainly legendary in Steelers' lore, or Bob Stoops who is a legendary OU coach, Spurrier who is a legendary Florida coach and legendary SEC coach, and even a man like Coach Stallings who was and is a legendary Alabama coach, but they don't have the multiple national titles that would cement them with the greats of all time.
No doubt, winning multiple titles today is harder than it ever was, both in college and in the NFL. College scholarship limitations that didn't exist in previous eras and almost universal TV exposure which has created a great deal of parity. The NFL has expanded numerous times since the days of Lombardi and also has free agency and a salary cap that the teams of the 70's and 80's (and before) didn't have to contend with.