Defenceman Tim Ramholt also scored for Omaha, while goalie Curtis McElhinney turned in a stellar performance in front of an announced crowd of 6,100 at Air Canada Centre.
Blueliner Richie Regehr chipped in with three assists for the Knights, who improved to 9-2-1.
Left winger Colin Murphy provided the lone marker for the Marlies as they dropped to 5-7-1.
With the annual Royal Agricultural Fair at Ricoh Coliseum until Sunday, the Marlies got a chance to play in the home of their NHL affiliate, the Toronto Maple Leafs, but couldn't overcome Omaha's special teams.
The Knights jumped out to a 3-0 lead on three power-play goals in the first period - two by Boyd - and also added a shorthanded marker - also by Boyd - in the second.
McElhinney was sharp throughout the game, stopping 32 of 33 shots for the victory. At the other end, Justin Pogge made 13 saves on 17 shots.
The Knights went 3-for-6 on the power play, while the Marlies were 0-for-7 with the man advantage.
The Marlies' next game is Saturday, when they face the visiting Hamilton Bulldogs in a matinee game at Air Canada Centre. The puck drops at 12:30 p.m. (ET).