When you say "Right Now" you are 5'3"; does that mean you intend to grow? I assume you are a girl by your screen name. How old are you? If you were a boy at age 14, then there's definitely a good possibility that you would probably grow maybe 5 more inches. Medically speaking, most girls can grow in height until about 18-19 years old. Boys around 20-21. However, the majority of girls stop growing around 16 and boys around 18. (This is from my College Anatomy instructor).
So, depending on what your age is, you might not even have a problem. However, the military academies have sort of changed their medical requirements. They don't actually rate you "Pilot Qualified" when you apply to the academy. That will come later around your 3rd year when you start applying for such duties as pilot. In that case, you will have a couple of extra years to get that extra inch or so you need.
Now matter how you look at it, your first priority is to get accepted to the academy. Hopefully, you aren't questioning applying based on if you have a chance at being a pilot. I'm assuming you are applying because you want to be at the academy and serve your country. And if you can't be a pilot, then that's OK. So, first things first. Get accepted to the academy. There isn't a thing in the world you can do to change your height; other than using gravity boots every night. But then, I don't think you'll get an inch. Good luck.