Yonkers rapper Jadakiss is busting up the charts with a song charging President Bush was a Sept. 11 conspirator.

“Why did Bush knock down the towers?” asks the song “Why?”, which comprises several dozen questions on subjects ranging from Kobe Bryant to the new $20 bills.

“Why?” jumped from No.33 to No.16 on the national Billboard charts last week, with a corresponding rise in controversy.

The conspiracy-theory Bush line is not seen in the video on MTV. The line also has been removed by many radio stations around the country, though both major hip-hop stations in New York play the full version and say they have heard no complaints.

“I didn’t even know there was an edited version,” said Tracy Cloherty, program director of WQHT-FM (97.1), which played “Why?” 54 times last week. “If [“Fahrenheit 9/11″ director] Michael Moore is entitled to his opinion, why not Jadakiss?”

“He’s just exercising his freedom of speech,” said Michael Saunders, program director of WWPR-FM (105.1), which played “Why?” 26 times. “There’s no reason to edit the line out.”

The 29-year-old Jadakiss took a shot last week at stations that do, saying, “They’re censoring me all over the place and that’s good. It means I’m reaching everybody.”

While Republicans and talk-radio hosts attacked the line, local music fans yesterday seemed largely unconcerned.

“His opinion is that of the ‘hood,” said Chuck Black, 24, who works at Ali CD’s on W. 125th St. “As far as us ‘black folks,’ we’re not offended by it.”