There are so many ways to quantify this.
If someone said to me the best programs now, its Bama Clemson OSU.
If you want to go to the BCS era broadly, bring in the Florida and LSU types.
If we want to extend to the poll era broadly, now you are including the ND and USC and Oklahoma types.
Best teams all time is a very different answer to me, and yes, it includes the teams that were great in the early part of the 20th century including Ivys.
Auburn is a top 15 or so program. But not really any higher.