I'm a grad student living in university housing in NYC for a few years but my permanent address is Long Island. Do I say I live in NYC or Long Island?

You will want to use the same address you used on your W-2s or any other income documents. 

If you're talking about the "mailing address" you enter under the Personal Info tab, you should use the address of where you live "right now", as that is the address the IRS will send any correspondence to concerning your tax return.

Ah ok.  This makes sense.  Thanks for a speedy response!