What kind of food is he getting? Switching to a super premium food (innova, ca natural, wellness, etc.) can help eliminate breath and body odor.

For more info try: http://www.api4animals.org/79.htm
http://www.ourpetfood.com/comparison.html

If you're already feeding this food, I apologize! I've never had a puppy, so I don't know what breath is normal.