The Seals’ impressive 2-0 victory was secured by goals from Charlie Caton and Elliott Whitehose.
The defeat left the Iron five points off National League North leaders Tamworth while Chester moved to within two of the play-off places.
McIntyre was thrilled by his team’s performance but said after the game that he feels Scunny will end the campaign as champions when all is said and done in April.
He told the Non-League Paper: “I thought we deserved the victory with two fine examples of top-class finishing that deserves to win any game.
“I consider Scunthorpe as the team who will win the league, so to record a victory against a very good side makes me extremely pleased.”
It was a fourth win in a row for Chester in all competitions, and their sixth victory in seven matches.
But on Tuesday night comes a real test of the club’s promotion credentials as they travel to a Southport side inspired since Jim Bentley’s arrival.
McIntyre says he knows how demanding the trip will be but says his team have been “fantastic” in October and called for more of the same as they head to Haig Avenue.