NY tax law treats the telecommuter working from home for a NY company to be working in NY and their income is taxable in NY.  Your income is 100% taxable in NY if this is the case.  Since PA also taxes your income, you will want to prepare the NY return first so you can claim a credit for the taxes you pay to NY on your PA return.

On the PA return, you should see a screen entitled "Confirm PA Wages" with an Edit link next to the Company Name on the W2.  Click on it, and make sure that the box is selected to make the NY income not taxable in PA.  If your W2 has both a NY and a PA line, PA tax programming requires both lines to be added together, and you must check that box so that your income is not double-reported to PA for the correct taxable amount.