Could be mange, which isn't unusual for pups. Have your vet take a scraping when you go. Also take in a stool sample to make sure there are no worms in his system.
Dogs should not have any vaccinations when they have any type of health issues going on, which your sweet little guy does, so please reconsider until this is cleared up and he is healthy. Also, if he was neutered recently, his immune system has taken a hit which is another reason not to vaccinate now.
He is a cutie!