I am a step-mom of an 11 yr-old boy who says he wants to live with us, but his mom is very manipulative and lies/threatens him to keep him with her. I understand the torment your little family is going through.
I don't agree completely with "let his father handle this" because you are also a figure in this boy's life. Yes, you have no legal right to what happens and depending on how much your boyfriend allows your interaction, it all limits you, but you are there for both the guys in your life. And your boyfriend chose you to be a part of his and his son's life, so I believe that you do have a little right to give input and your opinion.
What I tell my step-son is, "I am not your mother, but I am your friend and I love you and always want whats best for you." Your step-son loves his mother and big brother, but like you said, he has no idea that what was done to him was wrong. Let him know that you understand that he feels bad about what his mom says and as his friend, that you always want what's best for him and that you love him enough to want to keep him safe. And at this time, it is not safe for him to be at his mom's house.
Is there a way to limit contact with Mom at all? Can you record the conversations between Mother and Son? This could help you possibly to keep Mom from screwing with his mind. What Kaye S. said about it not being admissible in Court without her knowledge is true. But you just let her know, during a recorded phone conversation, that all communications will be recorded. Maybe she will stop calling, might think you're bluffing, or whatever...but the point is, if you let her know that you're recording, it can be admissible, whether she thinks you're joking or not.
And let your boyfriend know that you are with him 100% to keep his son safe and happy. Your support is the biggest thing that is needed right now. And what ever you do, try to support him in never backing down from this. This is for the safety and wellbeing of his son! And you guys are very smart not to say anything bad about Mom in front of the boy. Hopefully your struggles won't last too long as he is a little older, but either way, I wish you all the luck in the world from one step-mom to another. God bless you and yours.