I'm working in Midtown for the summer and I'm taking the train in from Newark NJ. My commute is about an hour because I have to take two different subway trains. Find out where you're going to be working and find a train or subway line that runs nearby. Then figure out how long you're willing to commute and what's the most you'll pay for rent (usually an inverse relationship). Here are some cheaper options if you don't mind living in Jersey.
If you're working midtown on the west side...live in Newark...it'll take you 10 mins to get to NY Penn Station and trains run frequently
If you're working around Wall Street...live in Jersey City...it's a quick commute on the water taxi.
Personally, I plan on moving to the city when I graduate because I'll be working long hours. If you're working a job that requires long hours, you'll probably be compensated accordingly and should move into Manhattan so that you have a life. If you're not working long hours, live in Jersey where you can keep your car.