In general, you pay state income taxes where you live, regardless of where you work or where your employer is based.
7 states have special rules for telecommuters, but MA is not one of them.
If you were previously a resident of MA, and moved temporarily to NY (such as for COVID) then MA will continue to tax you as a resident. NY will also tax you as a resident if you live there more than 183 days, even if your move is intended to be temporary. This is a situation where you should seek professional expert assistance.
However, if you have never been an MA resident, the fact that you take a new job with an MA-based employer does not change the fact that your permanent residence is in NY and that's where you pay state income tax.
Finally, if you do work occasionally in MA, you should expect to file an MA non-resident tax return to pay state tax on income earned within MA. You will get a credit on your NY return for taxes paid out of state. For example, if you are required to attend meetings 1 day every 2 weeks at the company office in MA, MA will consider that 1/10th (1 out of 10 business days) of your income is earned "in-state."
