Check with your employer as to how they are handling it. If you do not claim NY income for those three months and get audited, you’d have a stronger position if your company backs you.
Among the facts in the convenience of the employer test is: The employer does not provide the employee with designated office space or other regular work accommodations at one of its regular places of business.
TSB-M-06(5)I
It certainly seems you were performing remote work for those three months due to the necessity of the employer.
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