Cuomo's office will also be looking into mounting losses at the investment bank prior to BofA's purchase and any threats federal regulators may have made if the deal wasn't completed, a charge officials at the Charlotte, N.C.-based bank have made.

The subpoenas come as Cuomo is preparing to file fraud charges in coming weeks against several high-ranking executives at BofA in its acquisition of Merrill. The deal was hastily cobbled together a year ago just as Lehman Brothers was preparing for bankruptcy.

On Monday, a federal court judge rejected an agreement BofA reached with federal officials over the bonus matter and ordered a trial to begin Feb. 1. The decision by a U.S. District Court judge decision voids last month's $33 million deal between the Securities and Exchange Commission and the bank.

Merrill paid the bonuses despite losing a record $27.6 billion last year. Those losses showed up on the balance sheets of BofA, one of the largest recipients of funds from the U.S. government's Troubled Asset Relief Program, or TARP.