Honestly, I have no idea.  The website says "An applicant for licensure who met the eligibility requirements for grand-parenting under New York's 120 semester hour education requirements must document at least two years of full time experience (or the part-time equivalent)...providing accounting services or advice involving the use of accounting, attest, compilation, management advisory, financial advisory, tax, or consulting skills under the supervision of a certified public accountant licensed in one of the U.S. jurisdictions or a public accountant licensed in New York State."

Therefore, if your manager was a CPA in another state and just got licensed in NY via reciprosity, you are golden.

If he/she was not, give the board a call at 518-474-3817.  Don't give them your name, just explain that you have met your two years of experience, but your supervisor became licensed for the last 6 months, and ask what the implications are.  If they say that it is OK, ask them to send you an e-mail stating so.