doing the long distance thing is definitely possible, but certainly not easy. communication is key, and you have to expect that there will be ups and downs, good days and bad, but as long as you're committed to each other and put in the effort you can make it work.
my boyfriend and i have been apart for 2 years while i've been in grad school. the first year was only nyc--> boston (easy), but this year has been nyc--> san francisco, where he's doing his plastics residency. based on the fact that he's incredibly busy, and i know i'm going to be really busy next year, i've chosen to go to touro-ca (unless i get off the waitlist at one school which is close to home) otherwise, we would never see each other.
for your situation, i think it's good that only you'll be really busy for the first year you're apart - that may give her more flexibility in coming to visit you. for next year when she's applying, there are a ton of med schools in the new york metropolitan area so make sure she applies to ALL of them - it'll give you guys a better chance of being together. good luck, hope everything works out!