New York State Supreme Court Justice Bernard Fried ruled that the compensation figures didn't constitute a trade secret, as BofA had claimed.
Bank of America and the attorney general's office did not immediately comment on the ruling.
The judge's ruling reverses a temporary order keeping individual bonus information confidential. That order was put into place last month after Merrill's former CEO John Thain testified about the bonuses.
Bank of America bought New York-based Merrill Jan. 1.
Cuomo's office is trying to determine if Merrill and Charlotte, N.C.-based Bank of America failed to provide adequate disclosures to shareholders about the payouts, made in December, and the more than $15 billion in losses Merrill incurred in that quarter.
Merrill moved up its bonus payments to December from January to complete them before the sale to BofA.
Bank of America, which finds itself in Cuomo's cross-hairs, has repeatedly said Merrill was an independent company last year and it thus had no power to determine the size of payouts to Merrill employees.
During his first deposition, Thain refused to provide information about individual bonuses, claiming he was worried about a potential lawsuit from Bank of America. He was forced to return for a second round of questioning, though it is unclear if he gave details about the bonuses then.
Thain resigned as head of global wealth management at the combined company in January just as news of the bonuses broke.
BofA's CEO Ken Lewis testified last month as well, but did not reveal information about individual bonuses. During that testimony, Cuomo's office subpoenaed Lewis a second time in hopes of eventually getting the information.
In defending his position about the need to publicly release individual bonus information, Cuomo points out that Lewis said during his testimony that there has never been a policy at Bank of America that requires bonus information to remain confidential.
Cuomo and Rep. Barney Frank, D-Mass., sent a letter to Bank of America in early March demanding the information be made public because the bank has received $45 billion as part of the government's bank investment program. As a recipient of the funds, Bank of America must provide better transparency and disclosure to taxpayers about where their money is being spent, Cuomo and Frank asserted in the letter.
The initial reports of the bonuses came just days after Bank of America received an additional $20 billion from the government that the bank said it needed to help offset the losses it was absorbing from the Merrill acquisition. The additional support was provided as Lewis showed trepidation about completing the deal to acquire Merrill.
Frank, the chairman of the House Financial Services Committee, and other lawmakers have been insistent on knowing how financial institutions are spending taxpayers funds. Politicians have been indignant in recent days over bonuses paid to American International Group Inc. employees. The government bailed out the insurance giant last September and now owns about an 80 percent stake in the firm.
The government helped orchestrate the acquisition of Merrill by Bank of America over the same weekend in September that another investment bank, Lehman Brothers, went under and AIG received its initial government support.
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