I am a VT resident. If I make 1000 dollars in NY state as an independent contractor, and receive a 1099-MISC, do I need to file a NY return?

[DanielV01]

Probably.  NY will tax the income you earned in NY state.  If you earned enough income to have a filing requirement in NY (4,000 total income, not just NY income, if single, 8,000 total income if married filing joint), you will file a NY nonresident return.  VT will still tax the income, but will give you a credit for the tax you pay to NY on that income.