@edchen For you it depends. You are not required to file as Married Filing Joint in New York in your situation even though you file a joint Federal return. Please see this New York website: New York Married Filing Statuses. Since your spouse works in NYC, it probably is disadvantageous for your spouse to file as a full-year New York resident, since a New York city resident working in NYC is liable for the NYC local tax also. But, since you have options to file, then you certainly explore your options to see which option results in less tax and then use that one.
Filing a joint Federal Return and separate state returns can be a bit tricky. Usually it is better to use desktop software for this, because it will be necessary to mail in some of the returns (particularly your spouse's if you are the primary taxpayer on the return. This Help Article gives instructions on how to do this: How do I prepare a joint federal return and separate state returns?
However, and this is important, you almost certainly will need to use this technique for your spouse's separate New Jersey return. If you do not, then the system will try to turn your spouse's return into a New Jersey joint return (which might not end up in more tax, by the way, but will include your income). To file a separate New Jersey return, even if you end up filing a joint New York return, use the technique described in the Help Article.
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