New York uses the same filing status as you use for your Federal return, which is why New York is picking your return up as Married Filing Joint. Please see the following link for more information on the filing status in New York.
Filing status for New York
If you want to file in New York as Married Filing Separate, you will need to do the same for your Federal return.
Another option is to keep using the Married Filing Joint filing status, and then report a credit for the state taxes paid to DC.
In order to claim a credit for taxes paid to another state, you will need to complete your nonresident tax return first. In this case, you would select DC as your nonresident state.
Once you complete this, you will work on your resident return (assuming New York in this situation).
While answering the questions in the New York state return, you will see a screen for Credits and Taxes. When you reach this screen, locate the section titled "Credit for Taxes Paid".
- Select "Taxes Paid to Another State"
- Answer the questions until you reach "Other State"
- Here you will select the nonresident state where you paid taxes under "Other State"
- Select Continue after entering the state name.
- You will then be prompted to enter the portion of income taxed by the other state
- On the next screen, enter the amount of tax from the Other State
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