No NGO is sovereign. They may have members that are nations, but that doesn't mean anything.
To the extent that they do anything outside of sovereign territory within our country, they are subject to our laws. That would apply to any telephone conversations, or any other communications or actions.
We're not able to enter a foreign embassy and arrest anyone, but we can certainly arrest them when they leave it, unless they are a credentialed diplomat.
NGO's enjoy no special protection for anything they do.
Then maybe I'm thinking of IGOs?
http://www.uia.org/legal/app35.php