New York Attorney General Andrew Cuomo has set his sights on Bank of America honcho Ken Lewis, issuing him a subpoena to testify about what he knew about the 11th-hour bonus payments Merrill Lynch paid before BofA acquired the hobbled investment bank.

At issue is whether Lewis misled shareholders about his involvement with $4 billion in bonuses that were paid to Merrill executives just days before it closed its merger with BofA.

News of Lewis’ subpoena, which he received late last week, was first reported on The Wall Street Journal Web site.

Earlier this month, Lewis told Congress he had no authority to challenge the bonus payments, even though it appears details of the payouts were included in documents related to the merger.

Meanwhile, ex-Merrill boss John Thain spent all day yesterday being interviewed by Cuomo investigators.