NY is one of the odd states that doesn't always go with the flow. Yes, with many states, you pay taxes in the state where you perform the work and are physically present. However, a few states like New York have what is known as the Convenience of the Employer Rule which can potentially cause a remote worker to be taxed as if they were working in the state of NY while living in another state if they are working in the other state for their own convenience and do not meet several standards (see above link) to prove they are working remotely for the convenience of their employer.
@Leen1
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