Former Boston defender Pearson nodded home Scott Kerr's free-kick after 64 minutes before substitute McLaughlin struck in added time to cap an impressive showing from the Conference play-off hopefuls.
Northampton weathered an early storm but were struggling to create any clear-cut opportunities, with Jacob Blyth mis-hitting a long-range volley after 20 minutes.
Ross Hannah then wasted Grimsby's best chance of the first half when he blasted over from the edge of the area, before Cobblers midfielder Chris Hackett fired a free-kick over the crossbar.
Hannah tested visiting goalkeeper Matt Duke just before the hour mark and Kerr saw his goal-bound effort deflected over the bar by Kevin Amankwaah.
But Kerr turned provider to find Pearson at the back post, who looped his header beyond a hapless Duke to the delight of most inside Blundell Park.
Northampton, in the League Two relegation zone, tried to find a way back into the game but Blyth and Ian Morris both missed late chances before McLaughlin had the final say with the last kick of the match, converting Lenell John-Lewis' pass from close range.