USA State Payroll Rates + Resources: State of New York: Filing State Income Taxes, W-2s, and 1099s
Purpose
The purpose of this documentation is to outline the processes and requirements associated with filing state income taxes as well as how to file W-2s and 1099s, if needed, in the state of New York.
State Income Tax Withholding
Form IT-2104 is completed by an employee and given to the employer to instruct the employer how much New York State (and New York City and Yonkers) tax to withhold from their pay. If the employee does not file Form IT-2104, employers may use the same number of allowances claimed on the federal Form W‑4.
Due to differences in tax law, this may result in the wrong amount of tax withheld for New York State, New York City, and Yonkers. Employees should complete Form IT-2104 each year and file it with the employer if the number of allowances they may claim is different from federal Form W-4 or has changed.
Employees cannot use Form IT-2104 to claim exemption from withholding. To claim exemption from income tax withholding, employees must file Form IT-2104-E. An employee must file a new certificate each year that they qualify for the exemption. This exemption from withholding is allowable only if they had no New York income tax liability in the prior year, they expect none in the current year, and they are over 65 years of age, under 18, or a full-time student under 25.
If an employee who claims exemption from withholding on Form IT-2104-E usually earns more than $200 per week or claims more than 14 allowances, you must send a copy of that employee’s Form IT-2104-E to:
NYS Tax Department
Income Tax Audit Administrator, Withholding Certificate Coordinator
W A Harriman Campus,
Albany, NY 12227-0865
Since employees complete the withholding allowance form, employers must review the form to ensure the information is complete and legible. Employers must complete the form with their required information, including the employer’s name, address, EIN, whether dependent health insurance benefits are available to the employee and if so, the date the employee qualifies for the benefits, and the hire date.
The Tax Department will not accept this form if it is incomplete. They will review these certificates and notify you of any adjustments that must be made.
Due dates for sending certificates received from employees who claim exemption and earn more than $200 per week are the last day of the month following the end of the quarter.
State Income Tax Withholding Reporting and Deposits
Every employer paying wages or other payments subject to income tax withholding must file a return and pay the New York State, New York City, and Yonkers taxes required to be withheld.
Employers must electronically file withholding tax returns (NYS-1) and pay the withholding tax required to be withheld through the New York Business Express website.
Payment remittance & filing frequency:
| Frequency: | Accumulated Tax: | Due Date: |
| Frequent | More than $700 | 3 or 5 business days after the payroll that caused the accumulated tax withheld to equal or exceed $700. |
| Quarterly | Less than $700 | End of the month following the end of the quarter. |
See Withholding tax due dates.
Exceptions:
If you have more than one payroll within a week (Sunday through Saturday), you are not required to file Form NYS-1 until after the last payroll in the week.
When a calendar quarter ends between payrolls paid within a week, any accumulated tax required to be withheld of at least $700 must be remitted with Form NYS-1 after the last payroll in the quarter.
If you have filed at least once during the calendar quarter (using Form NYS-1) and have an un-remitted balance of tax withheld that is less than $700 after the last payroll of the quarter, remit this amount with your quarterly return, Form NYS-45, instead of with Form NYS-1.
New employers will be permitted to file and make payment of taxes withheld within five business days until notified otherwise by the Tax Department.
Quarterly Report:
You are required to report through New York Business Express, each calendar quarter, Federal gross wages subject to withholding and the total amount of New York State, New York City, and Yonkers tax withheld for every employee paid during the calendar quarter you are reporting.
This report is due at the end of the month following the end of the quarter being reported:
| Quarter | Months in Quarter | Due Date |
| 1st Quarter | January - March | April 30th |
| 2nd Quarter | April - June | July 31st |
| 3rd Quarter | July - September | October 31st |
| 4th Quarter | October - December | January 31st |
W-2 and 1099 Forms
Employers do not submit a copy of Form W-2 to New York State. Instead, employers must report quarterly wage and withholding information on each quarterly combined withholding, wage reporting, and UI return filed.
Employer requirements concerning the reporting of New York State, New York City, and Yonker wages on the federal form W-2, see pages 34 and 35 of the Employer's Guide to Unemployment Insurance Wage Reporting and Withholding Tax.
1099 Forms
Employers do not submit a copy of federal Form(s)1099 to New York State. New York State no longer requires the annual filing of Form 1099 information returns. However, New York State does require the reporting of Form 1099-R payments if there was New York State, New York City, or Yonkers income tax withheld.
For further details, see the Employer's Guide to Unemployment Insurance Wage Reporting and Withholding Tax.