Bongiorno told the jury she once asked how the firm was "making money when everyone else was losing money." She said Madoff told her they could make money in a down market by shorting stocks and she believed him.
Parise, the juror, said the testimony by Bongiorno and Bonventre "did not help their cause."
Clients lost nearly $20 billion. A court-appointed trustee has recovered much of the money by forcing those customers who received big payouts from Madoff to return them. When the fraud was revealed, Madoff admitted that the nearly $68 billion he claimed existed in accounts was only a few hundred million dollars.
The centerpiece of the prosecution's case was Frank DiPascali, Madoff's former finance chief, and five other insiders who pleaded guilty and agreed to cooperate.
At times, however, their testimony seemed to support the defendants' claims they were kept in the dark.
DiPascali acknowledged he lied to Perez and O'Hara "to trick them into working on the projects that he needed them to work on."
Attorney Larry Krantz, representing Perez, asked him if he was manipulating them so they could participate in the massive fraud without knowing it.
"Yes," DiPascali answered.
Defense lawyers, in their closing arguments, hammered at the notion that their clients were victims, too, losing tens of millions of dollars they had entrusted to their boss.
Attorney Gordon Mehler said his client, O'Hara, was "used, abused, manipulated, lied to, snookered and bamboozled" by two of the greatest criminal masterminds in history, Madoff and DiPascali.
Bongiorno's attorney, Roland Riopelle, said Bongiorno "saw $50 million of what she thought was her own money but was really Bernie Madoff's monopoly money go up in smoke. ... Ms. Bongiorno relied on Mr. Madoff, and she was fooled by him."
Breslin said Crupi was a victim of "the lies that they told her to her face, year after year."
The verdict was delivered after the jury deliberated for about 20 hours over a period of two weeks. The panel was down to 11 jurors after one juror became sick during deliberations and was dismissed.
The defendants were described by prosecutors as "necessary players" in Madoff's fraud. They said Bongiorno, hired in 1968, and Crupi, hired in 1983, used old stock tables to fabricate account statements and other fake records that kept the Securities and Exchange Commission in the dark. The government said they also rewarded themselves with tens of millions of dollars in salaries and bonuses, including $2.5 million for a beach house for Crupi as the Ponzi scheme was falling apart.
Prosecutors said O'Hara and Perez developed a software program that automated the fraud, generating "information out of thin air," as one put it.
The Ponzi scheme nearly ran out of money at least twice since the early 1990s before finally collapsing during the 2008 financial crisis.
During jury selection, prospective jurors were told that they might hear references to big names including Steven Spielberg, Sandy Koufax, Kevin Bacon and Zsa Zsa Gabor, among Madoff's victims. Hundreds of exhibits and thousands of pages of materials were put before jurors.
Also mentioned were Madoff's relatives, including his brother, wife and two sons. One of the sons committed suicide two years after the fraud was revealed.
Madoff, 75, is serving his sentence at a federal lockup in North Carolina.
Over the years, Alger Hiss and Julius and Ethel Rosenberg were tried as traitors in the Manhattan courthouse, and Khalid Sheik Mohammed's nephew Ramzi Yousef was convicted there in the 1993 World Trade Center bombing and in a plot to blow up a dozen airliners.
Associated Press writers Tom Hays and Jennifer Peltz also contributed to this report.