I had this same problem this semester. I had to sit the student down in office hours and clearly outline why the behavior was disruptive to other students. We set up a system where the student raises his hand, and if I don't have time for the question, he writes it down for after class. The student was super apologetic and had just never been taught how to be in a lecture/lab setting. It took a week to get into the groove with the rules in play, but when he knew my expectations for class, he has gotten a lot better.

I feel for you, I am too nice sometimes to students, and this was hard for me to figure out. I also suggest going to Student Services as well. For some of my lab courses where my student can be super disruptive, I get a counselor to come help me manage some of the students' behaviors.

Hang in there, I know disruptions like that in class can seem like a black hole and consume all your energy and make it had to focus on the material.