For purposes of filing your federal taxes with the IRS, your state of residency, and that of your spouse, does not matter. Your filing status at the federal level is determined by your marital status and whether or not you have dependents. If you are legally married, you may file as married filing jointly or married filing separately. In some cases, you may also qualify to file as head of household, even if you are legally married. In order to claim head of household status, you must be "considered unmarried" because your spouse did not live in your home for the last six months of the tax year and you have a child for whom you were the main support during the year.
New York General Rule
As a general rule, you must elect the same filing status for your New York state return that you claimed on your federal tax return. If you were not required to file a federal return, you must claim the filing status that you would have claimed had you filed a return.
There are three exceptions to the requirement that you choose the same filing status on your New York state tax return that you selected on your federal return. If you and your spouse are not both full year residents of New York, you may file separate returns, if you choose. In addition, if you are unable to locate your spouse at the time you prepare and file your New York state return, you may file a separate return. Finally, if your spouse refuses to sign your tax return and you are alienated from your spouse, then you may file a separate return.
How to File
The New York State Department of Taxation and Finance provides an online tool that can help you determine whether you are required to file a return and which return you must file if required to do so. You can also complete your return online through the website and file electronically in most cases.