Curt Gentry, author of Helter Skelter, also wrote a biography of J. Edgar Hoover where he states the same position, as well as its justification. In order to keep ostensible crime rates low, Hoover decided it was smarter to deny official recognition of an organized criminal organization. This way, incidents involving the mafia and ostensible suicides or accidents could be left untouched or as local crimes.

Adding onto this, Gentry even provides stories of either Hoover or high echelon FBI agents visiting the same barber as high-level mafia members, trading looks and quips about one another not existing.

Quoting from [this source] (http://history.stackexchange.com/questions/17326/why-did-j-edgar-hoover-publicly-deny-the-existence-of-the-mafia-for-so-long)

J. Edgar Hoover knew perfectly well that organized crime existed before 1957. In the 1940's he had been known to sit at the same table in upscale clubs with known underworld figures like Meyer Lansky.

He preferred to not acknowledge the mafia's existence so he would not be obligated to assign FBI agents to build cases against them. He chose to assign his agents to cases like unorganized interstate crime ("Pretty Boy" Floyd, John Dillinger, "Baby Face" Nelson), infiltrating the Communist party, and spying on and harassing civil rights leaders. It was only the blatant publicity of the Apalachin Meeting, after it was raided by state and local police, that forced the FBI director to admit that the mafia was an actual organization.)

Source:

Curt Gentry, J. Edgar Hoover (Also cited by the answerer in the link; if you find yourself looking for something to read after Chasing the Scream, it might be worth it.)