According to an indictment unsealed in federal court in Manhattan, Crupi, 49, and Bongiorno, 62, "'executed' trades in the accounts of (wealthy clients) only on paper ... and that achieved annual rates of return that had been predetermined by Madoff."
Prosecutors said that Bongiorno used a computer program programmed to backdate trades and manipulate account statements.
"I need the ability to give any settlement date I want," she wrote to a manager in the early 1990s, according to the indictment.
Prosecutors said Crupi created false documents to cover Madoff's tracks as he was being reviewed by the Securities and Exchange Commission.
According to seized records, Bongiorno deposited about $920,000 in her own Madoff account from 1975 to 2008. Records also show that she withdrew more than $14 million over the same period of time.
The indictment charges Crupi of receiving thousands of dollars in "off the books" income. Both women are charged with conspiracy, securities fraud and falsifying records.
Madoff is serving a 150-year sentence in federal prison after he admitted to operating his fraud for at least two decades, cheating thousands of individuals, charities, celebrities and institutional investors. Losses from his scheme are estimated at around $20 billion, making it the biggest investment fraud in U.S. history.
Both Crupi and Bongiorno face up to 20 years in prison if convicted of the most serious charges.
The Associated Press contributed to this report.