it get's complicated since your employer is located in NY and you are performing work for them for part of the year in PA. NY taxes telecommuters - those that work out of state for NY employers but could just as easily performed the work in NY. A case on point.
Section 601(e) of the New York State Tax Law imposes a personal income tax on a nonresident individual’s taxable income that is derived from New York sources. The tax is equal to the tax computed as if the individual were a New York State resident for the entire year, reduced by certain credits, multiplied by the income percentage.
Naturally, this law has been challenged. In Huckaby v. New York State Division of Tax Appeals (04-1734), a New York state court found Thomas L. Huckaby liable for taxes on 100% of the wages he earned from a New York employer while working from his home in Tennessee, which has no state income tax. Although Huckaby, a computer programmer, worked approximately 25% in his employer’s New York office, he admitted he worked from home most of the time for personal reasons. The New York Court of Appeals, the state’s highest court, upheld the decision. To be exempt from New York taxation, such wages must entail “duties … which by their very nature, cannot be performed at the employer’s place of business,” the court said.
While most states apply a “physical presence” test, New York applies a “convenience of the employer test.” In other words, in New York the income must be earned by work performed out of New York State for the necessity of the employer, rather than out of convenience.
so if your work could be performed at the company's NY offices you'll be taxed in NY and NYC on all the income earned from this employer. In addition, because you now reside in PA, you'll owe income taxes on the income earned while residing there. Pa will grant a full or partial taxes for a portion of the NY taxes you paid on the income you earned while a PA resident.
you need to make sure that your employer is withholding both NY and PA taxes.
