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Generally - as you work in NY - you should pay NY state taxes and your employer is obligated to withheld state taxes based on your work location.
As you are living in NJ - any income despite its source would be taxable in NJ. At the tax time - you will file NY state tax return as non-resident, and NJ state tax return as a resident. On your NJ tax return you will claim the credit for taxes paid to NY - so you would not have the same income taxed twice.
If you need me to estimate your withholding - please specify what is your gross pay and how are you paid - weekly/biweekly.
Assuming you files W4 as Single with 1 allowance and paid beweekly
from gross pay $59,225 in NJ your paycheck should be
Gross Pay -- $2,277.88 Federal Withholding -- $375.20 Social Security -- $141.23 Medicare -- $33.03 New Jersey -- $73.34 SUI/SDI -- $21.07 Net Pay -- $1,634.01
from gross pay $67,000 in NY your paycheck should be
Gross Pay -- $2,576.92 Federal Withholding -- $449.96 Social Security -- $159.77 Medicare -- $37.37 New York -- $140.24 NY SDI -- $1.20 Net Pay -- $1,788.38
I noticed $100 difference with what your check used to be for $1534 after tax - that may be because you have additional withholding such as health insurance, union dues, 401k, etc - please verify
Assuming all the same - the deference should be ~$150 per pay period - please verify numbers on your paycheck stub.