What school do you go to? I go to Rutgers and I heard that Calculus 3 here is easier than Calculus 1 and 2, so you should definitely check on that first. Noone can answer you for sure about whether Stern would look down upon that or not. I recommend posting this on the official NYU forums where you will get an answer from an administrator. But, I would assume they do look upon it. I understand you don't like math that much, but you must have some sort of affinity for it, seeing as you got a 5 on the AP Calculus BC exam.
Also, I'm planning on transferring to NYU Stern for Fall '10 as well. Well, planning on applying, that is. Hello, competition.