Yes. Although I guess that depends what kind of ceremony they have, Time Lords might not have mothers in law.Never thought of that... But, if he ever did (not that he neccesarily will), then yes, Amy would be his mother-in-law, and Rory his father-in-law.
Even if Time Lords don't have the same traditions as we do, the Doctor knows the human traditions and might not be able to resist teasing Amy about being his mother-in-law. It's certainly something that will occur to Amy sooner or later -- and it's not quite what she had in mind at the end of "Flesh and Stone"! Remember that, when Amy first met River, her guess was that River was the Doctor's wife, not just a girlfriend.