You need to file a New York (NY) state resident tax return and a Connecticut (CT) non-resident tax return. When you enter your W-2 you will fill out the state information for the first state listed on your Form W-2. You will then add a state and fill out the information for the second state. As a New York resident, they will tax your income regardless of where it is earned. Connecticut has a Convenience of the Employer rule that applies to states that have a similar rule (which includes New York). Connecticut requires New York residents who work remotely for a Connecticut employer to file a nonresident tax return reporting all income. New York will give you a credit for taxes paid to other states (In your case Connecticut ) so the income is not double-taxed. The credit amount may be the same or less than the CT tax you pay, but it will not be more.
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