I work for a large bank and we have several employees who would be out on the street in a second if they let unlicensed software on our computers. Their job is to mantain records and bill departments for the licenses. With a small buisness that really can't afford the licenses, I would just make sure you had proof (written memos) that you raised concerns about the practices and try to get them to make it a priority to fix as soon as the cash is available.
Or make sure the owner knows he will lose his buisness if any anonymous person reports you to the BSA... Few people have no enemies (ex-wives and their lawyers are big risks). Don't lose your job over this though, tough economy out there...