Part 1 – Complete this part to calculate your withholding allowances for New York State and Yonkers (line 1 of Form IT-2104). Im kind of seeing it now.The IRS views any bonus you receive as wages. This means that almost all bonuses are taxed. Learn how to run a bonus payroll and accurately calculate bonus pay and taxes with our comprehensive small business guide. This New York bonus tax calculator uses supplemental tax rates to calculate withholding on special wage payments such as bonuses. The IT2104 form is an essential document for New York employers when it comes to payroll administration. One of the most effective ways to reduce taxes on a bonus is to reduce your gross income with a contribution to a taxdeferred retirement account. A payroll calculator New York businesses trust to get employees' paychecks right. Your W-2 Wage and Tax Statement itemizes your total annual wages and the amount of taxes withheld from your paycheck.