So I contacted NYITCOM admissions, and he said they value the 2 science letters more than the non-science letter. He also said it can most likely count towards non-science if he taught you both science and non-science courses (but I don't know what my professor wrote so.. haha). Either way, it doesn't sound like they will throw out your app if you don't have the non-science letter. I have a call into PCOM as well, that might be a different story, I heard they are more strict.