It was SIU without a doubt. They won more regular season championships than Creighton. CU finished 1st or tied for 1st 3 times, while SIU finished 1st or tied for 1st 5 times. To me winning the regular season is more impressive. So with that, most of SIU's NCAA tourney invites were at-large invites.
SIU went to the NCAA tourney 6 times (3 times advancing past the 1st round and 2 of those were Sweet 16). CU went to the NCAA tourney 5 times (Only advancing past the 1st round 1 time)