We talked about this late last year- AE Degrees.

I would see where you can get accepted first, starting from the list provided in that thread, and then figure out the flying part as a second priority. It is a safe bet that any good engineering school is going to also have a flying club, however flight training for credit may be harder to find. I never got any credit for my flight training; it was just something I did to have fun, flesh out my aerospace studies, and use as a second career which as it turns out was prescient considering the economy. ERAU has it, but beyond that I cannot say who has both an AE and a flight training curriculum. Time to do some homework. Let us know what you find out.