My husband is military and is not filing in Virginia. is his income part of VAGI?

[Phillip1]

No.

If your spouse is not a Virginia resident and you are, you must file a separate VA tax return. This will only include your income as Virginia AGI. You will need to prepare a full separate Federal and state return for the one tax needs to file a VA resident tax return.

See the following from Virginia - Military Tax Tips:

Filing Separate Returns

If you are a resident and your spouse is a nonresident (or vice versa), you and your spouse must file separate returns. Income, dependent exemptions, and itemized deductions must be allocated under federal rules for separate filing, as if you had filed separate federal returns. As a general rule, the spouse claiming an exemption for a dependent must be reporting at least half of the total federal adjusted gross income. In addition, the spouse must be able to support his/her claim of itemized deductions. If it is not possible to account for the deductions separately, the deductions may be allocated based on each spouse's share of the federal adjusted gross income. When filing a separate return, the other spouse's income, exemptions, and deductions should not be included.

[ArmyWife]

Thank you for this answer!  Now that I know I do not need to include my military spouse's VAGI, how do I remove the entry I made previously? (I entered his income from Box 1 of his W-2 since I wasn't sure what to put, but since he was not a Virginia resident anytime during the tax year, I now need to remove the entry I made previously).  

[DMarkM1]

When you build your "Mock" federal return with Married Filing Separate status you will only put in your income in the federal "Wages and Income" section.  This will not include any of his income on your return.  Then in the VA state interview in the "Credits Section" you will find the "Low Income Credit" topic.  There you will verify/adjust the income so that you spouse's income is not in the calculation for that credit.

Having said that be sure you need to file in VA at all.  If you are the spouse of a military member and your spouse is in VA on military orders and you are there only to be with them and his home of record (resident state) is in another state then you can elect to have your resident state match his and your income earned as an employee in VA would not be taxable in VA either.  

In other words if your military spouse is not filing in VA due to his military status and VA non-residency then you can do the same.  

Here is the VA reference.