incorrect NY state income allocation

It depends on the reason you became a remote employee whether or not you need to correct your allocation on your nonresident NY return. 

If you became a remote employee for your convenience, then it is still NYS sourced income and the allocation should be 100%.

On the other hand, if you became a remote employee for your employer's convenience, then the allocation should be corrected and you should amend both your NY and NJ return. In this case, you would amend your NY return for the allocation and the NJ return for the credit of taxes due to another state. Even if the net difference is minimal, it is still important that your allocations are corrected. 

In addition, your home office in NJ must meet at least four secondary factors as well as at least three other factors in order for your income to not be sourced in NYS when you are telecommuting.

Secondary factors include:

• Your home office is a requirement or condition of your job (for example, you were hired as a full-time, remote employee and your employer requires you to have a dedicated home office space).
• Your employer has a legitimate business purpose for your home office location (for example, your employer sets up a satellite office to service customers in a specific region).
• You complete some of your job's the core duties at your home office (for example, patient notes, billing or admin-related work).
• You meet with clients, patients or customers on a regular and continuous basis at your home office.
• Your employer doesn’t provide you with designated office space or a regular work area at one of its regular places of business.
• Your employer reimburses the expenses for your home office.

Other factors include:

• Your employer has a separate telephone line and listing for your home office.
• Your home office address and phone number is listed on the business letterhead or the business cards of your employer.
• You use a specific, separate area of the home exclusively to handle business for your New York State employer.
  • Note: The home office will not meet this requirement if the area is used for both business and personal purposes.
• Your employer’s business is selling products and you’re responsible for keeping an inventory of the products in your home office.
• Business records for your employer are stored at the your home office.
• Your home office location has a sign which includes your employer's business name.
• Your employer's advertisements shows your home office as a place of business for your employer.
• Your home office is covered by a business insurance policy or by a business rider on your homeowner insurance policy.
• You’re entitled to, and claim a deduction for home office expenses related to federal income tax.
• You aren’t considered an officer of the company.

For more info, review the Application of the Convenience of the Employer Test to Telecommuters and Others, Is my remote income taxable in New York State? and What is the convenience of the employer rule? 

If you need to amend your state returns, please see How do I amend my state returns?