Small doesn't mean unhealthy! Pyrs vary greatly in size. When I was at the Great Pyrenees National Specialy Show in April, I saw a few males that were 27" tall and others at 32" tall with weight variance of 85-130 lbs. Breeders also often say that pups that are small at birth do not always stay small at maturity. Thus if your vet thinks the pup is healthy and growing at a reasonable rate, I would think you are doing fine
There is this another possibility that perhaps your pup may have a bit of a smaller breed mixed in him. You had said that he has only single dewclaws and that while the breeder told you he's a purebred, you didn't actually see the parents. I have a male pyr mix that could have passed for a purebred pyr as a little pup. At 8-9 weeks he was about 11 lbs.