This is a really hard decision. I'm sorry you have to worry about this, but I'm glad you are thinking about it this far ahead.
IMO I think you should bring Boomer home with you. I think you would miss him terribly if you left him behind.
Another thing to consider is that if you leave Boomer behind with another military family the day will come when they will have to go and probably leave Boomer behind again. And it could possibly happen again and again.
I would compare one bad day to every three years flipping families. The time could come that a nice family could choose the shelter as an option if they can't find a good home for him.
My ex was in the military for awhile so I do understand how limited your choices are but I would take these other things into consideration.
I'm sure you will do the best thing no matter what you decide because you are a good meowmie and love Boomer very much.