In his autobiography, Joe Bonanno claims his cousin, Stefano Magaddino, the don of Buffalo, kidnapped him because Magaddino was jealous of Joe's rise to power and was siding with the Commission in its dispute with Joe. Gay Talese, in his book about Salvatore (Bill) Bonanno,"Honor Thy Father," never really answers the question, though he gives a hint.
But the gangland.com site provides this insight:
"In October 1964, on the night before he was to appear before a federal grand jury looking into the upstate conclave [the famous Apalachin, NY meeting that was busted by the cops], two gunmen forced him into a car as he was walking with his attorney. For Bonanno, it was a great time to make himself scarce – family wiseguys were on his case for trying to make son Bill the family consigliere; the Commission was furious Bonanno had plotted to kill two of them – and not too many people thought he had been kidnapped."
Furthermore, the hint Talese provides in his book reproduces part of an FBI wiretap. two days later, of the phone of Sam (the Plumber) DeCavalcante, who was a Commission go-between in their efforts to get Bonanno to explain his apparent backing of an earlier coup (the attempted rubout of Carlo Gambino and Tommy Lucchese). DeCavalcante said on the tape:
"He [Bonanno] pulled that off himself [i.e., the kidnapping]...Well, who the hell is he kidding? He kidded the government..."It was his own men...we figured it was his kid and Vito De Filippo...This guy has got a lot of government appearances...but he left everybody in trouble."

You decide. Seems to me that Bonanno had ample reason to engineer his own disappearance. In 1929, Al Capone engineered his own arrest on a concealed weapons charge, and spent a year in a Pennsylvania prison, because things were getting too hot for him in Chicago and the rest of the country's mobsters were anxious for him to take a powder.