Unfortunately, probably both.
New York state has a "Convenience of the Employer" tax rule. What this means to you is that all of the work for a New York employer, whether you are physically there or working remotely, will be taxable to New York.
Since you are a resident of Pennsylvania, all of your income, regardless of its source, is also taxable there as well.
The silver lining is that you are able to claim a credit on your Pennsylvania tax return for the taxes paid to New York.
I hope this helps.
Ryan