It should make no difference who is listed first on the tax return. The discussions about different amounts refer to situations where listing one person first will create a resident return while listing the other person will create a non-resident return.
In your situation, since you both work in New York, all your income is taxed by New York either way.
Depending on your income and deductions, you may be better off filing separate New York returns. If there is a big difference in income, a joint return may push you into a higher tax bracket.
On the other hand, if you both own homes and pay mortgages, you may get a better joint itemized deduction by filing together. Unlike the federal return, New York does not limit your deduction for state and local taxes to $10,000.
Regardless, file a separate Pennsylvania return. PA has a flat tax with no deductions or exemptions, except for a deduction for unreimbursed work expenses.
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