First off, I'm glad to hear you're going to stick with the nursing. Hearing that is a hard one...
Next, is your son healthy otherwise? Other than looking "small" does he appear to be healthy and thriving? Bright eyes, round cheeks, healthy looking skin, a decent amount of meat on his "small" bones? I know that growth is a very legitimate concern, so please don't think I'm dismissing yours in any way! Just asking questions...
You mention that he's always been on the smaller side... Other mamas correct me if I'm wrong, but doesn't the concern come when they're "suddenly" going from a high percentile, to a low percentile? Or when they're in a high percentile for height, but not weight, etc.? It sounds like your son has always been a smaller guy... What about you and your partner? Are either of you very small people? Were either of you very small children?
Upping calories isn't necessarily the worst thing to do. I think the ice cream suggestion is absolutely ridiculous, but fats are good for little kids. Their brains and bodies need plenty. If your son is about 1 year of age, he's only going to get more and more active as the year progresses. Don't be afraid to put butter on everything! YOU probably wouldn't want to eat butter on everything (or maybe, shouldn't eat butter on everything), but your brain and body is done growing.
If you really think your son is unhealthy, and you really do want to up his caloric/fat intake, a few higher calorie ideas (assuming no food allergies):
-avocados, and plenty of them
-replacing the water to boil oatmeal with whole milk, or even half whole milk and half heavy cream. It makes for some decadent oatmeal!
-adding a bit of coconut oil to whole milk yogurt, or soy yogurt
-scrambled egg fried in a generous dollop of butter or olive oil
-homemade alfredo is a huge hit in our house. Add cream, butter, parmesan, and garlic to some whole wheat or quinoa pasta, and viola!
-cream added to smoothies
-fattier cuts of grass-fed beef or lamb, slow cooked in a crock pot or the oven until they're falling apart.
-homemade hummus with plenty of olive oil (or you can buy the store stuff and just blend in some extra oil)
-don't be afraid to butter those veggies!! sweet potatoes with generous amounts of butter or coconut oil! Or melt some good cheese onto broccoli. And we love pureed cauliflower with lots of butter and parmesan.
-when you serve fruit, serve it with cheese. Or whip up some cream and just leave out the sugar. My DS looooves dipping his berries in whipped cream.
-Not just peanut butter, but almond butter, cashew butter, etc., all have lots of fat. Tahini is a good option too.
Those are what leap to mind right now. But I would stress, too, to look less at the charts, and more at overall health. Some kids are just smaller, or more active. If your son eats happily, and appears healthy (and just being small doesn't mean a child is unhealthy), then it's possible that he is just a small little guy. You mentioned your ped is looking in to other issues? Can you share what they were? It might help to offer more direction...
Good luck to you, and happy eating!