How old is he? New puppies are going through a LOT of changes; whole new environment, Mom and siblings are gone, new people, new experiences...a whole new world. Give him some time to come around. It's possible that his breeder didn't do a lot to expose him to different sights and sounds and experiences and so he's not sure how to cope with these now.
As an aside, a toddler is scary for MANY dogs, not just puppies. They're loud, they're rough, they boldly run right in and want to play. I would suggest that you perhaps gate the puppy off away from your son for the first few days while he becomes adjusted to his new home. In all likelihood, in a few days he will start to realize that this big new world isn't out to eat him, and he'll relax. You can provide lots of praise for him in the meantime, and don't go out of your way to take him to a bunch of different places right away (he probably isn't fully vaccinated anyways, right?). Let him enjoy being home with you for a week and reevaluate his behavior then.