I'm an army military intelligence officer. I have dealt with security clearances and this sort of thing for almost 12 years now.
Your sister is full of fucking shit.
Here is how this works: Your sister meets your boyfriend. She goes to the security office at NRO and says "Hey my sister is dating this foreigner. Here is his name, country of birth, and citizenship status. What do you need me to do?"
I am 99% certain that the answer will be "Here, fill out this piece of paper called an Additional Foreign Contact Sheet." She'll call you for the info (name, DOB, place of birth, occupation, how often she interacts with him etc etc etc). It is pretty basic stuff. She'll have to answer a question whether he or his immediate family (mom, dad, siblings, children) work for or have ever worked for a foreign government or military, and if the answer is yes, she might have to provide their names, DOB, and POB. She'll have to verbally promise that if you or he ever attempt to get classified information from her that she will report it to her Security Office. That is all. There is no fucking investigation, there is literally one goddamn piece of fucking paper.
I'm assuming he went to West Point or one of the other military academies here, which will only help him/her/you, because it means that he has been fully vetted by the United States government, and when they stick his name in the database, he'll pop up. This means there is either a problem with him, or he's been vetted. They'll see he went to the Academy and go "huh. let's go to lunch."
If you guys get married she'll have to update the security office and say "hey, OP and foreign boyfriend got married." At that point, they will likely want to know what are his plans for citizenship, etc etc etc.
Seriously. He has to be from an allied, friendly, or neutral country because otherwise the Military Academy wouldn't have accepted him; we don't do foreign exchanges with enemy countries. Even if he had been from somewhere a little more questionable, as long as he wasn't connected with a Foreign Intelligence Service they'd have put his name in the computer and that would be the end of it.
My entire family are foreign. Granted, western Europeans and South Americans, but I am literally the only motherfucker besides my dad that lives in the USA or has citizenship: EVERYONE else in my family is a foreign national living in a foreign country. I still have a TS and work at NSA.
To be honest, either I'm really disappointed in your sister's complete lack of knowledge at the rank of E6 (particularly if she works at NRO, she should have some fucking clue), or there is some other reason she doesn't want to meet him and was banking on you not knowing any of this information.