We let him claim our son basically for the years rent. I just wasn't sure if he would have to also claim my wife in order to claim her son or if he can claim the son and me my wife

Well, as I said, since you were there over 6 months it's OK to do it that way.  But I suggest that you look at what your refund would be if you claim her son and have him figure out the value of claiming him  I'm guessing that the tax benefit of him being on your return would exceed the other, in which case you can give him that part of your refund.