New York payroll service, handled end to end.
New York payroll service from Long Island, for employers across New York State.
PayNortheast runs payroll for New York employers from start to finish: New York State, New York City and Yonkers withholding, quarterly NYS-45 filing, Paid Family Leave and disability deductions, and the pay rules that are specific to New York.
New York payroll, done for you.
For employers on Long Island, in New York City and across New York State, PayNortheast handles the setup, every pay run and every New York filing.
- Fast, guided setup with free data migration
- New York State, NYC and Yonkers withholding, filed for you
- Quarterly NYS-45 prepared and e-filed
- Paid Family Leave and disability deductions on every pay stub
- A real person to talk to
Good fit if you’re…
- Paying employees in New York City, Yonkers or on Long Island
- Need weekly pay for manual workers
- Tracking MCTMT, Paid Family Leave or regional minimum wage
Payroll services for New York employers.
Every New York payroll requirement below is part of our full service payroll, with a dedicated account manager from day one.
New York State withholding
We withhold New York State income tax on every payroll from each employee’s Form IT-2104, and keep it current when employees move, marry or change jobs.
Quarterly NYS-45
Withholding, wage reporting and unemployment insurance, combined on one quarterly return that we prepare and e-file for you.
NYC and Yonkers tax
New York City resident tax and Yonkers resident and nonresident tax, withheld alongside state tax and reported on W-2s.
PFL and disability deductions
Employee Paid Family Leave and disability (DBL) contributions taken in payroll at the current rates and shown on every pay stub.
Unemployment insurance
State unemployment contributions calculated at your assigned rate up to the annual wage base, and reported every quarter.
MCTMT for downstate employers
The Metropolitan Commuter Transportation Mobility Tax, tracked by zone each quarter for employers in New York City and the surrounding counties.
How New York employers run payroll with us.
Run it online, send it to us, or customize your own process. Same dedicated contact behind every one.
Online Portal
Process payroll and manage your team online, anytime.
Email or Text
Simply send us your hours. We do everything else.
Custom
Payroll as unique as your business. We build it around how you work.
“I want to enter the payroll. You enter the new hires.”
“I just want to send you the hours from my point of sale. You do the rest.”
“I want you to enter the daily logs, add the hours to payroll and add new hires.”
“Pay my staff automatically every payroll. I’ll let you know if anything changes.”
“I want to run everything myself online, but have someone to call when I need help.”
Tell us how you want it. We’ll build it. Let’s Chat →
New York pay rules, built into every payroll.
New York sets its own rules for how often you pay, what you tell new hires and what every pay stub shows. We set your payroll up to follow them.
- Manual workers paid weekly, and clerical and other workers at least twice a month
- Wage Theft Prevention Act pay notices at hire, with rate, pay basis, regular payday and employer details
- Pay stubs with pay dates, rates, gross wages, deductions, allowances and net pay
- Paid sick leave accrued and tracked on every payroll
- Minimum wage set by region: New York City, Long Island and Westchester, or the rest of the state
Where New York payroll gets specific
- Different pay frequencies for different groups of employees
- Employees who live in New York City or Yonkers
- Employers with staff across the downstate counties
- Prevailing wage and union work on public jobs
On public works jobs, see our prevailing wage and certified payroll service.
New York State payroll taxes and rates for 2026.
The New York numbers we build into payroll this year, from the state agencies that set them.
| Item | 2026 rule |
|---|---|
| New York Paid Family Leave | Employee contribution of 0.432% of gross wages per pay period, up to $411.91 for the year (2026).Source: paidfamilyleave.ny.gov · PFL deductions guide |
| New York disability (DBL) | Employee contribution of one-half of one percent of wages, up to 60 cents a week.Source: wcb.ny.gov |
| New York unemployment insurance | Employer-paid on each employee’s wages up to $17,600 (2026 wage base). Total 2026 rates run from 1.7% to 9.5%, and new employers pay 4.1%, each including the 0.075% Re-employment Service Fund.Source: dol.ny.gov |
| MCTMT (downstate) | Applies to employers with more than $312,500 of payroll expense in a calendar quarter in the Metropolitan Commuter Transportation District. Rates depend on the zone and the payroll expense in it, filed quarterly on Form MTA-305.Source: tax.ny.gov |
| Minimum wage | $17.00 an hour in New York City, Long Island and Westchester, and $16.00 in the rest of the state. Some industries, tipped workers and home care aides have different rates.Source: dol.ny.gov · Minimum wage regions guide |
| Paid sick leave | Up to 56 paid hours a year with 100 or more employees and up to 40 paid hours with 5 to 99 employees. Employers with 4 or fewer employees provide up to 40 hours, paid if net income was over $1 million. Accrual is at least 1 hour for every 30 hours worked.Source: ny.gov · Paid sick leave guide |
Rates change. We update them in payroll when New York does, so you don’t have to track them.
New York payroll reports, ready when you need them.
New York employers on Long Island, in New York City and across the state get clear payroll reports after every run, without building spreadsheets.
- Payroll registers after every pay run
- Pay stubs and earnings statements online, including PFL and disability deductions
- NYS-45 and payroll tax filing summaries
- Year-end W-2 reports
For you and your accountant
- Quarterly and year-end packets for your accountant
- Reports by department or location as you grow
- Year-end payroll checklist for New York
- Full service payroll reporting
We can generate any report you need. Tell us what your accountant or auditor is asking for and we’ll put it together.
Payroll that integrates with the tools and programs you already use.
PayNortheast integrates with timekeeping, accounting software including QuickBooks, job costing and certified payroll platforms, and with workers’ comp through partner carriers, 401(k) and retirement plans through partner providers, and state programs such as New York Secure Choice. We also integrate with POS systems, including tips and hours imported, custom data feeds and file imports, HR and new hire onboarding, and benefit and union fund reporting.
Payroll for your industry.
Industry payroll for businesses on Long Island, in New York City and across New York State, with the same dedicated contact behind every one.
New York payroll, explained for employers.
Guides on the rates and rules we build into New York payroll, plus year-end and training resources.
Minimum wage regions
Minimum wage for New York City, Long Island and Westchester, and the rest of the state, including tipped and home care rates.
Minimum wage regions →Paid Family Leave deductions
How New York Paid Family Leave deductions work: rates and caps, the pay stub line and employer duties.
PFL deductions →Paid sick leave
Accrual, 40 or 56 hours by size, carryover, pay rate, records and paid prenatal leave.
Paid sick leave →Weekly pay for manual workers
Who counts as a manual worker, when wages are due, and New York’s weekly pay rule.
Weekly pay rules →Year-end payroll checklist
W-2, 1099, 941, 940 and NYS-45 deadlines, holiday paydays, bonuses and January 1 rates.
Year-end checklist →ITIN payroll for New York employers
How to pay employees who hold ITINs once they are authorized to work, and why an ITIN never replaces an SSN on a W-2.
ITIN payroll →New York payroll FAQ
Do you handle New York City and Yonkers withholding?
Yes. We withhold New York City tax for employees who live in New York City and Yonkers tax for Yonkers residents, plus Yonkers nonresident earnings tax where it applies, alongside New York State withholding, based on each employee’s Form IT-2104.
Who files our NYS-45 each quarter?
We do. Form NYS-45 combines New York State withholding, quarterly wage reporting and unemployment insurance in one return, due April 30, July 31, October 31 and January 31. We prepare and e-file it for every quarter.
Do you sell Paid Family Leave or disability insurance?
No. Your Paid Family Leave and disability coverage comes from your insurance carrier. PayNortheast takes the employee contributions through payroll at the current rates and shows them on every pay stub.
Are we subject to the MCTMT?
It depends on where your employees work and how much payroll you have there. Employers with more than $312,500 of payroll expense in a calendar quarter across the Metropolitan Commuter Transportation District, which includes New York City, Nassau, Suffolk, Westchester, Rockland, Orange, Putnam and Dutchess counties, are subject to it. We track it each quarter and tell you when it applies.
Can you pay our manual workers weekly?
Yes. New York requires manual workers to be paid weekly unless the employer has state authorization to pay less often. We run weekly, biweekly, semi-monthly and monthly payrolls, and different schedules for different groups of employees.
Let’s talk about your New York payroll.
Tell us where your employees live and work and how you pay them today. We’ll show you exactly how PayNortheast would run your New York payroll, or contact us with a question.
Free account setup when you switch