The PA/NJ tax reciprocity applies only to employee compensation that is subject to withholding, and it does not apply to city or local taxes. Therefore your 1099-MISC earnings will be subject to PA state income tax, as well as any Philadelphia city tax. Therefore you should make your estimated tax payments to PA and if necessary to Philadelphia.
Your 1099 income will also be taxable by your home state of NJ, but you'll be able to take a credit on your NJ return for taxes paid to PA.
References:
https://revenue-pa.custhelp.com/app/answers/detail/a_id/851/kw/PA%2FNJ%20reciprocity
http://www.state.nj.us/treasury/taxation/njit25.shtml
**Answers are correct to the best of my ability but do not constitute tax or legal advice.
