Travel To NYC ....Amtrak or Bus

I, too, will vouch for the hostel on Amsterdam Avenue. I've worked in the neighborhood for years, renovationg co-ops for people who would not spend in excess of a million dollars for their properties if the area were sketchy. And since you say you're in college, I'll take the liberty of mentioning that the "scenery" at that hostel can't be beat.

At $29 per night, you'll save more than enough to make the "right" choice regarding transportation. All aboard Amtrak.

Amtrak's not always the best option so you might have to take what you can get. And if you have the time you can still catch trains in action at Sunnyside Yard or on the subway... It's not as good as an Amtrak train but it's still a great experience.