Some states allow you to file Federal jointly, and then State joint too, with a way to remove the non-resident spouse's income in the state section interview
From what I see in the NY instructions on the NY website...I don't see that NY allows that, and you would have to prepare and file NY as MFS.
Using the desktop H&B software you would start a new tax file for yourself, as a Federal MFS tax return, and then go thru the NY MFS questions. The MFS Federal would not be filed, and you would then have to print and mail-file the NY-MFS tax return to NY. (Yes, NY frowns on it, bu mail-filing is allowed when you cannot e-file the NY part...and you cannot e-file NY since your Federal-MFS cannot/must not be e-filed if you are filing Federal MFJ.)
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With the Desktop Software, You do have the option to prepare both of your tax returns both MFS-Federal and MFS-State as two separate file sets.....and they could all be e-filed if you decide it work s out OK......but that is usually NOT recommended since some credits and deductions are not allowed when you do that, AND both spouses must use the Std Ded, or both must use Itemized deductions (even if itemized deduction is zero for one spouse). Std Ded is now pretty high, so that might work out anyhow.
Since you indicated you are using desktop H&B software, you could easily prepare MFS-Fed&NY and MFS-Fed&MD as separate tax files without submitting them, and compare the MFS-Federal results to MFJ-Federal to see what the differences are (I have no idea if MD allows MFJ-Federal combined with an MFJ-MD with a way to remove the non-resident spouse's income for the MD part)
____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*
