New York has a "convenience of the employer" rule for telecommuters.  Generally, the New York Department stated that "if you are a nonresident whose primary office is in New York State, your days telecommuting during the pandemic are considered days worked in [New York] unless your employer has established a bona fide employer office at your telecommuting location."

You most likely will pay nonresident New York state taxes, but this is a very complicated tax issue which is beyond the scope this forum.  

 The "bona fide employer office" exception is narrow, meaning that most work-from-home employment still would be treated as New York-sourced income. Pursuant to New York Department memorandum TSB-M-06(5)I, for tax years beginning in 2006, a day of work spent at a home office is treated as a day worked outside of New York "if the taxpayer’s home office is a bona fide employer office." To be considered "bona fide," an employer office must satisfy either (1) a primary factor or (2) at least four secondary and three other factors. The primary factor is that the "home office contains or is near specialized facilities." Secondary factors are the following: (1) the home office is a condition of employment, (2) the employer has a bona fide purpose for the home office location, (3) the employee performs core duties from the home office, (4) the employee meets or deals with clients regularly at the home office, (5) the employer does not provide the employee with a designated office space at its regular places of business and (6) the employer provides reimbursement of substantially all expenses for the home office. Other factors are (1) the employer maintains a separate telephone line for the home office, (2) the home office address is listed on business letterhead, (3) the employee uses a specific area of the home exclusively for the business, (4) the employee keeps inventory of products or samples at the home office, (5) business records are stored at the home office, (6) the home office has a sign indicating that it is a place of business, (7) advertising for the employer lists the home office, (8) the home office is covered by business insurance, (9) the employee is entitled to home office expense deductions and (10) the employee is not an officer of the company.