Your federal is easy with MFJ. You both have income in PA, Did you fill out REV-419 so that only NJ tax was withheld or was PA tax withheld? NJ and PA have a reciprocal agreement.
I am going to assume that you had NJ tax withheld since you live there and your wife had PA tax withheld.
NJ and PA also understand that you could work in one and maybe live in one or two states. PA will allow you to tax all income and then NJ gets a credit for the portion earned by you in NJ. See more here.
For NJ, as a resident, you must use the same filing status as federal. You will mark your spouse's income as earned out of state to qualify for a credit against your NJ return. See NJ instructions here.
In plain language you need to:
enter federal MFJ
prepare PA resident MFJ to create the tax lability
prepare NJ resident MFJ showing only your resident NJ income since it was all from PA. Get a credit for tax paid to PA
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