My boxer got into something, I don't know what but she broke out in hives - got all puffy too. I gave her Benadryl but it wasnt enough, she had to go to the vet. He gave her a light sedative to sleep the rest of the day and some good allergy meds.
It could be bites from fleas or similar. You will more than likely need to take him to the vets and get a strong product to wash him in however be very careful with the puppies eyes. The bumps could be a rash from a particular plant you have in the garden. Take note if the bumps make the pup chew on them as they will only aggravate the problem. Skin problems in pets is very uncomfortable for them as they are in humans so a trip to the vets beckons.