Hospital is probably connected to the State retirement system, which is why there are no SS wages or withholding and the military has their own retirement system also.

Are you filing him as a non resident of NY, but still liable for taxes on income earned in NY?

His military earnings, I believe, would still be exempt from NY taxation, because his residency is temporary and not related to his military service requirements.

Hopefully someone with more experience in this area and NY regulations will respond to this post and confirm or correct what I believe. NY is a bit crazy so you want to get it right the first time,