Rooney, who had not found the net since the Champions League quarter-final first leg against Bayern Munich, converted a first-half penalty after Ryan Giggs was brought down by Jonathan Spector.
Nani doubled United's lead five minutes into the second half with a superb finish from Rooney's clever lay-off and Dimitar Berbatov completed an easy victory with a rasping volley to leave West Ham without any points and bottom of the table.
"It was good Wayne got the goal but his performance was the important thing for me," Ferguson told the club's website.
"He enjoyed his football and was full of energy. That's good because he's not had a lot of football and he had a virus last week. But he trained all week and looked more like himself."
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