Well first of all, out of nowhere he talks to me saying "Why are you working for the Legion?"

Which I am confused why he asked that, because I'm not working for them? How do I get out of their control, if I am and didn't know it?

I want Boone back, but now he just goes to my Lucky 38 suite and every time I try to talk to get him to be my companion again, he just says "I lost all the respect for you" and that's all.

What do I do!?!

I wanted to side with the NCR, not the Legion. What do I do?

check to see if youre wearing Legion armor... if so take it off... any faction armor you wear shows that youre associating with them...

Haha definitely not wearing Legion armor, don't even own any...

I am liked by both the Legion and the NCR, so... Apparently being liked by Legion makes Boone mad at me. So how do I lower my rep with Legion, and just work/be liked for NCR?

Go hunt some legion dudes, make them hate you.