Stallion,
The only way to know if they will accept you and your eyeballs is to ask. From what I hear they are accepting more eye conditions now than they were when I was applying in the early 90's. They are even allowing (and paying for) certain types of eye-surgeries - for pilots even! That was unheard of just a couple of years ago.
What year are you in school? It's not too early to begin the application process for both the Academy and ROTC. Apply to everything to keep your options open until it comes time to make a decision.
E-mail me and I will answer any of your questions about the Academy, outline the admissions process, and get you in contact with the admissions department if you aren't already. I don't know much about applying for ROTC since that's not the route I took, but the information is out there and shouldn't be too hard to get your hands on.
JohnZ - You've been there and done that - thank you sir.
Semper Fi,
Culprit