Champions United were three goals up after 25 minutes thanks to one from Javier Hernandez, making his first start of the season, and two from Rooney who has scored in every Premier League game this term.
Hernandez added another for the visitors in the 58th minute before Rooney struck his third 10 minutes later to complete back-to-back league hat-tricks.
"They [Rooney and Hernandez] are a constant threat. Their movement and the pace they play at was really first class for us today," manager Sir Alex Ferguson told ESPN television.
Like two weeks ago, when City recorded a 5-1 win at Tottenham Hotspur only to be trumped by United's 8-2 thrashing of Arsenal, Ferguson's side outgunned Roberto Mancini's team to sit top of the table above City on goal difference.
City prospered against Wigan thanks to Argentina forward Aguero who has six goals in four games for his new club but any headlines he might have received were soon overtaken by United's masterclass at Bolton.
Hernandez opened the scoring in the fifth minute with the type of finish that was a hallmark of his debut season last year, making a fantastic run into the box to get an outstretched leg to Nani's cross from the right.
Two quick goals by Rooney, both deft touches set up by defender Phil Jones, put United three up at the break as Bolton's defence fell apart.
Hernandez, who missed the start of the campaign after suffering concussion on a pre-season tour, showed last term's great form was no fluke as he slotted in from close range after Bolton failed to clear in the 58th minute.
Rooney completed his hat-trick with a superb first-time drive after a pull-back from Nani while Hernandez missed a couple of chances to snatch his own treble.
United's day was clouded by Tom Cleverley limping off in the opening minutes with Ferguson saying the midfielder may have broken his foot after a "bad tackle" from Bolton captain Kevin Davies.
BEING ECLIPSED
While Rooney and Ferguson said United were concentrating on their own game rather than worrying about City, fans from the blue side of Manchester will find it galling that their excellent start to the season is being eclipsed.
Displaying a more attacking brand of football than last season's more conservative approach, Mancini's men took just 13 minutes to get off the mark at home to Wigan with David Silva and Carlos Tevez combining well to put Aguero through.
Tevez missed a penalty and City wasted several other chances before substitute Samir Nasri, playing with a broken finger, put Aguero through with his first touch of the ball in the 63rd minute.
Six minutes later Aguero completed his hat-trick when he tucked in another through ball from Silva to give his side plenty of confidence before they make their Champions League debut at home to Napoli on Wednesday.
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