It depends. What determines whether or not your income is taxable in New York depends on whether it is New York Source income. There are two types of income that New York considers to be New York Source:
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Wages Earned In New York State. This is fairly simple: you are working within New York State borders, so New York has the right to tax you for the income you are earning inside of New York.
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Telecommuting for a New York Company conducting business in New York State. New York argues that telecommuting (working from home) is for the benefit of the employee, so the income is being produced in New York and is therefore taxable to New York. If you telecommute, and your employer has established with the state that your work is for the employer's convenience, then your telecommuting income is not taxed in New York.
Otherwise, the fact that you work for a New York company does not in and of itself make your income taxable in New York. You must be working in New York for it to be New York income.
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