Jordan Huff added 128 yards rushing, including a 53-yard scoring run in the second quarter, on 13 carries.
Northern Illinois (5-3, 3-1 Mid-American) rushed for a season-high 322 yards on 59 carries - its second straight game with at least 300 yards rushing. The Huskies improved to 11-1 when rushing 55 times or more.
Hare had three touchdown passes in the first half as Northern Illinois took a 35-0 lead into the break. His fourth, a 39-yarder to Tommylee Lewis, made it 42-7 midway through the third.
Bouagnon topped the 100-yard plateau for the fourth-consecutive game and fifth time this season.
Darius Jackson finished with 101 yards rushing and two touchdowns for Eastern Michigan (1-7, 0-4), which has lost eight in a row against Northern Illinois.