I think you are wise to watch carefully and be ready to intervene. Your boy sounds like a good big brother but he could hurt the puppy inadvertently. It sounds like he is being very restrained and good with her. I know exactly how you feel though. I brought home a 6 week old kitten and looked over to see my Lab girl, my wonderful Jet , doing the same thing to the kitten. Not the growling but she was nibbling his neck. The kitten appeared to be not only unconcerned but actually to be loving it. Still, I supervised all their interactions till kitten was older.
Oban, my current Lab, is very good with puppies. He is afraid of such young ones and avoids them but when they get to be little shark monsters he'll do the exact same thing and he hasn't hurt a puppy yet. Still, again, I supervise.