Your CPA should figure this out for you. The CPA has the full picture of your tax situation.
How much you have to pay Pennsylvania will depend on how much time you actually spent working in Pennsylvania. Income from working in New York for a Pennsylvania client is not Pennsylvania income. If you never worked in Pennsylvania at all, you do not have to pay any Pennsylvania tax. But income you earned for work you did in Pennsylvania is Pennsylvania source income and you have to pay Pennsylvania tax on it.
Since you are a New York resident, if you do have to pay any tax to Pennsylvania you will get a credit on your New York resident tax return for part or all of the tax that you pay to Pennsylvania.
New York City tax does not apply to nonresidents of the city, even if you work in New York City.
