United moved above Chelsea and Arsenal, who are in FA Cup fourth-round action this weekend, with 50 points from 23 games.
Arsenal have 48 from 22 matches while Chelsea are also on 48 having played two games fewer than United.
Rio Ferdinand returned to the centre of United's defence after being sidelined by a back injury since a 2-0 defeat by Liverpool in October but was relatively untroubled as the hosts dominated third from bottom Hull.
It was the first time Rooney had scored four goals in a match in his senior career, with three of them coming late on as Hull's resistance crumbled.
"Wayne Rooney was the undoubted highlight of the match," manager Alex Ferguson told MUTV.
"It's the first time that he's scored four goals for us. That is very pleasing and he is in excellent goalscoring form at the moment.
"He'll beat his previous best (season) tally of 23 goals, I'm sure of that. He's in excellent form. It's only encouraging for Wayne because he's wanted to develop himself as a scorer."
While Rooney took his league tally for the season to 19, Ferguson also praised Michael Owen who started alongside Rooney for just the fourth time since joining from Newcastle United.
"I thought he did well today alongside Michael Owen. There was good movement and hunger. They did well," Ferguson said.
Rooney took just eight minutes to put United ahead, pouncing on a rebound after Boaz Myhill failed to hold a shot from midfielder Paul Scholes.
United were not totally convincing until the final 10 minutes when Rooney caught fire. His second was a fierce drive after being set up by Darron Gibson.
He sealed his hat-trick with a header from Nani's cross and rounded off his one-man demolition of Hull with a classy fourth.
