first, i'm guessing you accidentally left out bama in the all time listing. homer in me had to call it out.

second, imo the blue bloods are in both lists. so that's bama, osu, ou, nd, usc, texas, and mich, probably in that order. so that's 7 right off the bat.
for all time, i'd just add the next few closest, with a slight lean to those more recently successful. miami, fsu, florida, uga, psu, neb, lsu and clemson. just missing cut were tenn, au, aTm, mich st, washington, wisconsin, pitt, army, navy and maybe oregon.
for current, i'd add to the blue bloods, with heavy weight to recent success (last 10-20 years): clemson, psu, au, oregon, florida, uga, wisconsin, lsu. just missing cut, aTm, fsu, tcu, boise, ucf, stanford, ok st, and va tech.
final caveat, for some of them that were really close, i leaned toward balancing regions.for example, if tenn and neb in the all time list were really similar and could pick either, i went with neb because the se region was already really heavily represented.