It might be fitting for his dad to introduce this matter, during a casual conversation they are having about other topics -- family matters, school, current events, etc. He might say something like, "You know son, I'm really happy about how you and your stepmother get along. In fact, I sort of get the impression that you might have kind of a crush on her. I can understand how if I were 13 I might end up having a crush on someone who is pretty and kind and makes everyone she sees feel good. Those are some of the things that attracted me to her. I had a crush on one of my teachers when I was your age. About 100 other seventh- and eighth-grade boys and I wanted to marry her. Then we found out that she was married and that threw a wrench into our marriage plans. It must feel sort of strange having a crush on your stepmother. It's not quite the same as having a crush on a teacher." After Dad makes such a statement that shows understanding and doesn't shame or embarrass his son, maybe there can be some talk about how the boy feels about his stepmom and his crush on her. Let's not forget that the boy might not be very inclined to surrender up the fact that he has a crush on his father's wife. What's important is that the father gets this out in the open in a very supportive, understanding way.
Your friend can't forbid her stepson from having a crush on her. However, if she does begin to feel uncomfortable about his behavior toward her and her best efforts to deflect his attentiveness don't work, she might need to sit down with him and kindly say out loud what they both know is happening and how although she is flattered by his attention that it is making her a bit uncomfortable. Since I don't know how recently she became his stepmother, how she knows that he has a crush on her, or the temperament of the boy, it's difficult for me to give more detailed advice. Maintaining a close, loving relationship with her stepson, while not fueling his crush on her, should be her goal. This is not a problem unless and until it becomes a continuing discomfort for your friend and an unnatural romantic attachment for this boy.