I've been in somewhat of the same boat, I was stationed in CA for about 8 years and am legally a New York State resident. I can't think of too many states that you will have issues moving the pistols to with the exception of New York. If your wife doesn't have a permanent residence in NY it is doubtful that she will be able to get a NYS permit.
Slightly unrelated but I try to pass it on to all military New Yorkers. If you live off base, you are exempt from NY State income tax.