New York State says of your situation, "In general, unless your employer specifically acted to establish a bona fide employer office at your telecommuting location, you will continue to owe New York State income tax on income earned while telecommuting."
So you will file a New York non-resident return. Even without the New York entries on your W-2, TurboTax will use the federal income to start the New York return.
Normally, you would do the non-resident state (NY) first, then do your resident state (MA). You should see a dollar amount appear on line 30 of Form 1 (MA), which represents your New York tax as a credit to MA. This is how many states avoid double taxation.
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