One quick and interesting visual we can use to determine if these two teams are comparable is a tree of NIU's wins from this year and last year. For simplicity's sake, a team is included in the tree only once, and at the point where it has the fewest degrees of separation from NIU.
Here's this year (full size):
And here's last year (full size):
If you count it all up, NIU this year is connected by winning to 123 teams or every team in the FBS except two: Ohio State and Florida State. Last year, however, they were connected to only 105. However, we also see the Iowa loss (noted by the red X) from last year's tree. How bad was that loss? Well, we could now look at the tree of losses for last year to get a sense.
NIU's 2012 Loss Tree (full size):
Bad. Through losses, originating in their one loss to Iowa, NIU in 2012 was connected to 116 teams (more than through wins). Not good, and they shouldn't have gone to a BCS bowl. But NIU this year is undefeated. Not only are they undefeated but in their tree of wins they are connected to every team with at least one loss in the country: Alabama, Auburn, Oregon, Stanford, Missouri, Oklahoma State, etc.
So why not NIU? Obviously last year they were ranked too high, but this year, evidence suggests they are ranked too low. The voters and the more tautological ranking systems may not agree, but from an evidence based perspective, if Ohio State or Florida State were to lose, NIU has a case to make.