It depends.
Assuming you are living in Virginia and she is residing in New York, then yes, it would make more sense to file your federal return as Married Filing Joint to ensure you get the most tax breaks, but then filing separately for state based upon your states of residency and sources of income from each state.
Both state returns would need to be mailed in.
For New York, please see the following link for more instructions. You can file using the Married Filing Separately status as you did not reside in New York for the entire year.
New York filing status
For Virginia, you can also file separately. Please see the attached link for more information on this state.
Virginia filing status
Please see the attached link for instructions on how to prepare your state returns.
How to File MFJ for Federal but separately for state
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