Michael Reddy's second-half strike was enough to take Grimsby to the top of League Two, at the expense of Boston.
The Irish striker volleyed Andy Parkinson's cross past Conrad Logan from close range.
Boston should have taken the lead in the first half when Jamie Clarke forced Steve Mildenhall into making a save.
United's Chris Holland fired over the crossbar from close range, while Boston boss Steve Evans was escorted from the dug-out by police in the second half.
Grimsby: Mildenhall, Cohen, Robert Jones, Newey, Croft, Parkinson, Woodhouse, Toner (Gary Jones 78), Barwick (Kamudimba 67), Reddy, Mendes.
Subs Not Used: North, Murray, Downey.
Booked: Reddy, Kamudimba.
Goals: Reddy 72.
Boston Utd: Logan, Silk, Greaves (Hall 45), Canoville, McCann (Thomas 77), Till, Clarke, Talbot (Rusk 29), Holland, Keene, Joachim.
Subs Not Used: Maylett, Dudfield.
Ref: P Armstrong (Berkshire).