NY income tax shoulkd be withheld from your pay check - you submit form IT-2104 to your employer. Copy here: http://www.tax.ny.gov/pdf/2011/fillin/wt/it2104_2011_fill_in.pdf

No need for NJ tax to be withheld. If you have other sources of income you may need to file an estimated tax form with NJ each quarter - form NJ1040-ES: http://www.state.nj.us/treasury/taxation/pdf/other_forms/tgi-ee/2009/101040es.pdf

Thanks for your reply! So, I should not file the IT-2104.1? The one for nonresidence? I will have rental property income from different state. But it will probably be a loss after all expense and depreciation. So, do I still need to file estimated tax for NJ? Thanks again!

A. Form IT2104.1 is intended for non-resident employees who work only a portion of the time at an office in NY. If your primary place of employment is in NY State, then use IT2104.

B. If your only other income is from a rental property that has a loss, then it is unlikley that you will have to pay any NJ income tax at all. It sounds like you are a new employee, and perhaps new to NJ - if so then for the first year there is no penalty if you happen to end up owing tax to NJ at the end of the year. So I suggest that you go this first year without filing any estimated tax forms with NJ, and then see at the end of the year when you file your NJ income tax whether you owe anything.

I have little trouble fill out the IT-2104 form. Since I do not live in New York. What should I put down as total number of allowances for New York City (line 2)?

You are not a resident of NYC, so you are NOT subject to NYC resident income tax. You can leave line 2 blank, as long as you properly check "No" to being a NYC resident.

Oh cool! That was easy! What would be your recommendation for line 1? Total # of allowances you are claiming for NYS? I am single and I don't have any credits I would claim on my return beside I own a rental property in different state.

Read the directions that come with the form. It seems that on line 1 you list how many dependents you have - which for you sounds like 0.