Yes you will have to fill out a NY non-resident tax return. All of the money you earn from your company is taxable in NY. However, if you have obligated out of state duties (travel) that amount can be deducted. You will get a credit in Massachusetts for the taxes paid in NY. You do not have to pay NYC taxes.
Please review NY Convenience of the employer test to Telecommuters An excerpt of the law reads:
"Section 601(e) of the New York State Tax Law imposes a personal income tax on a nonresident individual’s taxable income that is derived from New York sources. The tax is equal to the tax computed as if the individual were a New York State resident for the entire year, reduced by certain credits, multiplied by the income percentage."
"However, any allowance claimed for days worked outside New York State must be based upon the performance of services which of necessity, as distinguished from convenience, obligate the employee to out-of-state duties in the service of his employer."
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