The agreement resolves all civil claims by the DOJ linked to the Swiss bank's legacy RMBS business in the U.S.
Ng was the only Goldman banker to face trial in the global scheme.
Lee reportedly died in his office on Thursday of a self-inflicted gunshot wound.
Firms that self-report possible white-collar crimes will be dealt with more leniently, federal prosecutors said.
Prosecutors said the scheme allowed executives to evade taxes on company-paid perks, including apartments and cars.
Ruja Ignatova is wanted for an alleged multimillion-dollar cryptocurrency pyramid scheme.
Goldman Sachs Group Inc.'s dirty laundry has been airing in a New York courtroom.
For both men, the most serious charge carries a maximum prison sentence of 20 years.
Rather than go after the scheme's mastermind, prosecutors targeted wealthy parents in the scandal.
William Singer spent more than $20 million of his money, some of it in furtherance of the scheme, a witness at his trial said.