You do pay income taxes (federal and state) when the work is done inside the United States, but you should not be paying self-employment tax, even though you are an independent contractor in this instance.
You don't want to back the income out again since it is taxable (federal and state) when you work inside of the US and are an independent contractor.
When the work is performed outside of the US, you are typically entitled to exclude much of it using the Foreign Earned Income Exclusion (FEIE) but the FEIE doesn't apply when physically working for the international organization inside of the US.
Workers who aren't citizens are exempt from US taxes when working in the US for certain covered organizations, and this typically also covers permanent residents except for independent contractors.
There is a good bit of information about taxation on employees and contractors of international organizations HERE.
In the link above, pay special attention to the heading "Exemption under US tax law" and the provisions for independent contractors.
Unless I misunderstand your situation, I believe this is what applies in your case that makes the income taxable.
If you were an employee, because you are not a citizen, you could be exempt as long as you haven't signed the waiver mentioned in this same paragraph.
However, because you are an independent contractor, the exemption doesn't apply except that you are exempt from the self-employment tax.
This area of tax, as you can see, is more complex than most!
**Say "Thanks" by clicking the thumb icon in a post
**Mark the post that answers your question by clicking on "Mark as Best Answer"
