I've got a pip-squeak of a kid, too. (Always in the 3-5% range for height) Ironically, the person most concerned was my 4'11" mother-in-law!!! (bless her heart). I'm 5'2" - husband is 5'5" - exactly where is she expecting these height genes to come from? That being said, my husband is somewhat concerned, because he grew up being a short kid, and he reminds me of how hard it can be during the teenage years. In fact, it wasn't until he was in his 30s that he finally came to peace with it.
We've got a book called "The Short Child" that would probably interest you. See if you can find it online. His thinking is "Yeah, even if he's perfectly healthy and normal, this world can be hard on short kids, especially when they are teenagers. If there is something I can do to change that, I want to at least consider it."
So the 4 year old got a "bone age" test last year, his pediatrician recommended it - "just in case", she said. (He was just over 37" at age 4, the 5th percentile.)
We had to go down to the Children's Hospital (GREAT interior design in the lobby, by the way!) and they took an X-ray of his hand - took maybe 1 minute and the the doc was able to look at the results immediately. Basically, the results were, yeah, he's short, but he's developing normally.
We've also looked a little at hormone therapy. Bascially, it's pretty controversial for children who are "normal, but short". If there's a problem with hormone deficiency, then therapy is more acceptable. For the "normal but short" kids, it may not be effective for one thing. Plus, from what I hear, it's a huge pain. (DAILY injections of hormones.) I am SO not ready for that. But do your own research.
Beyond that, it's basically "clean livin'" - exercise,
nutritious diet, plenty of sleep, and maybe a multivitamin or calcium supplement. (They now make these calcium supplements that taste like caramel candies.)
Personally, we struggle with the "diet" part, because my older kid seems to survive on 100 calories a day. He never seems to be hungry for more than 2 bites. (My husband says "Chris defies the laws of physics! He expends more energy than he puts in!") The "10 calorie kid" has become a running joke, and when he says he's full after just a few bites, we say "Well, I guess that will keep him alive until breakfast." I just have to make sure he gets something healthy in those 2-3 bites. Sometimes I can get him to have a protein smoothie.
A last note, sports can be difficult for small boys, and you may have to get creative to find something that he can excel at. It'll give him a little confidence to know that he's good at SOMETHING before they start doing those "Presidental Awards for Physical Fitness" or whatever they call them. Kids with shorter legs usually can't run as fast or jump as high, and I remember feeling pretty depressed when they did that every year at my school. I felt bad about any kind of sports for YEARS until I was 12 and I discovered I could swim like nobody's business.
Gymnastics/tumbling would also be good, and even some forms of martial arts are particularly designed for people with small statures (like Wing Chun). (My son saw an acrobatics show at the Renn fest, and now he's all excited to find a gymnastics class so he can learn to do that stuff.) If he's REALLY small, consider horseback riding lessons. Maybe he'll be a world class horse jockey! (Most of those guys riding in the Kentucky Derby are like 110 pounds.) :)