If this happened to me, I would sit down with this kid and his mother, (and also have my husband there since he saw the kid in your room), and tell them both that either he respects your whole family(incl your pups) or he is not welcome in your house. I would keep a close watch on him whenever he's in your house.
If you don't stand up for your family members, nobody will.
On second thought-
I've been thinking about this situation and I might be really tempted to just say that from now on he's not allowed at your house. If this is the kind of kid that sneaks into private areas of your home to antagonize family members (furry or not!), he might not be the kind of kid you want your son hanging out with.
Good luck!
__________________  Shannon & Puff 
"All his life he tried to be a good person. Many times, however, he failed; for after all he was only human. He wasn't a dog." Charles M. Schultz |