Lynch compiled 220 passing yards, going 16-of-35 through the air, and rushed for 83 yards on 15 carries for the Huskies (6-0, 2-0 MAC).
Cameron Stingily picked up 80 yards with score on 21 carries as NIU notched its 23rd consecutive home win.
Tommylee Lewis led the Huskies' receiving corps with six catches for 58 yards.
The Zips (1-6, 0-3), meanwhile, dropped their 30th straight road game as Kyle Pohl completed 24-of-56 pass attempts for 262 yards with a touchdown and an interception.
Jawon Chisholm scored twice on 21 carries, gaining 70 yards for Akron.