Tuesday's charges are the first tied to the JPMorgan attack, which compromised information in 83 million customer accounts in what prosecutors called the largest theft of customer data from a U.S. financial institution.
Authorities said Shalon and Aaron executed that hacking, using a computer server in Egypt that they had rented under an alias that Shalon often used.
E*Trade Financial Corp, Scottrade Inc and News Corp's Dow Jones unit, which publishes The Wall Street Journal, were also targeted by defendants in the case, a law enforcement source said.
Tuesday's charges also substantially expand a criminal case first announced in July, and cover alleged wrongdoing dating back to 2007.
Shalon, 31, and Orenstein, 40, are Israeli nationals who were arrested in July, while Aaron, 31, is a U.S. citizen who has lived in Moscow and Tel Aviv, authorities have said. Murgio, from Florida, was also arrested in July.
JPMorgan on Tuesday confirmed that the latest charges relate to the 2014 attack, and said it continues to cooperate with law enforcement efforts to fight cybercrime. E*Trade said it has contacted 31,000 customers who may have been affected.
News Corp's Dow Jones & Co, the publisher of the Wall Street Journal, confirmed in a statement that the indictment relates to a data breach the company disclosed on Oct. 9. In the October letter, Dow Jones CEO William Lewis wrote the breach focus was to obtain contact information of current and former subscribers.
Lawyers for the defendants were not immediately available for comment.
The new charges portray Shalon as the ringleader, having orchestrated nine hackings in which personal information for more than 100 million customers was stolen.
He and Orenstein were accused of having run at least 12 illegal Internet casinos, as well as payment processors IDPay and Todur, through which they collected $18 million of fees to process hundreds of millions of dollars of transactions for criminals.
According to the indictment, the illegal proceeds included tens of millions of dollars from manipulating the prices of stocks sold to customers whose information had been stolen.
Shalon was also accused of concealing at least $100 million in Swiss and other accounts, and running Coin.mx with Murgio.
The indictment against Shalon, Orenstein and Aaron includes counts of computer hacking, securities fraud, wire fraud, identity theft, illegal Internet gambling and conspiring to commit money laundering. Not all counts were brought against all the defendants.
Murgio faces seven counts including wire fraud, money laundering and operating an unlicensed money transmitter.
The U.S. Securities and Exchange Commission previously filed civil charges against Shalon, Aaron and Orenstein.