Good Afternoon -
Your post wasn't too clear on the issue - I couldn't tell if your employer was withholding Pennsylvania payroll taxes, or you personally were paying other Pennsylvania taxes; or if your employer was withholding New York payroll taxes.
However, the answer on unemployment is that you should be paid unemployment by the state you paid unemployment taxes to - which are the taxes withheld from your payroll. Your company's pay stubs should show which state taxes were being paid to.
Your company could have chosen to pay payroll taxes either to New York or Pennsylvania - either one was fine. I suspect your company was withholding New York payroll taxes - otherwise, you wouldn't qualify for New York unemployment.
However, if your company was withholding New York payroll taxes, you would have needed to file non-resident tax returns with the State of New York all along.
Ah, I see; I didn't read your last response carefully enough. Usually, companies will pay payroll taxes and withholding to the same state, so I made the assumption that the unemployment withholding was paid to Pennsylvania. Since it was paid to New York, you are fine.
I agree with the first accountant, not the second.