I think either will be fine but then again every once in a while some programs don't work on Macs. If you have Windows installed on your Mac with Boot Camp then you don't have to worry. Actually I really wouldn't worry just get the MacBook Pro.
Well, I'm not up at cornell yet, but I've had experience with both screen sizes. I used to have one of the old 12-inch powerbooks and loved the portability...and I just purchased a macbook pro (15 inch) for college with the extra screen size. I think both sizes will be fine for you. It rrealy is a matter of preference. Do you want something smaller (and with slightly less power), or do you want a more powerful machine with a biger screen that will be bigger and heavier and more expensive. Both of them appear to meet reqs for cornell and are sold at their store for pretty good prices.
just to post out of boredom, I use a 12" Powerbook G4 that I've had for about 3 years. It's the best, the portability is really why I bought it in the first place. I have books and binders that are heavier and larger.
Get a Macbook and then a 19inch LCD. The duo screen is Awesome. This combination gives you portability, screen size, and cheap price. One problem is.. I dont think I can use duo screen in the dorm room. Macbook's screen is bound to block the 19inch's.