If you qualify for the New York exemption, you will need to file a NY non-resident return to get a refund of any tax withheld. To qualify for the exemption, you must meet the following requirements:

1. You did not maintain any permanent place of abode in New York State during the tax year;

2. You maintained a permanent place of abode outside New York State during the entire tax year; and

3. You spent 30 days or less (any part of a day is a day for this purpose) in New York State during the tax year.

 --This includes any reason above for active duty military officials as well--

If you meet the requirements, as you work through your state return, change your residency status to Nonresident. 

When you are asked about New York Income Allocation, indicate that your wages were not all earned in New York State.  You will then land on the page titled "Your Form W-2 Summary", click Edit next to your DFAS W-2.  Next, indicate that you want to allocate the income by percentage and enter zero as the percentage.  That will exclude your military pay from NY tax.