I did not breastfeed, but i had the same problem w/ my son and it WAS acid reflux (if you haven't already, Google the term "GERD"). when he was about 2 months old, they put him on Prevacid (they tried Zantac first, but changed it) and since then, it's a world of difference. We have to watch what we give him a little bit - nothing too acidic, and I shy away from too much juice anyway b/c I'm diabetic myself, so I give him low-sugar juice, diluted, when I do.
Ethan also was VERY congested at that age. He grew out of it, and pretty quickly.
I really would try the reflux route - you said he doesn't spit up a lot, and that really clues me in! Ethan didn't either, and that was part of the problem; he should have been spitting up, and it was just getting trapped in his throat and made him sound congested in his throat, when really it was basically heartburn. His nose congestion was bad too, though, although like I said, he was small (5lbs 12oz) and his nasal cavities were just little and he outgrew it. Try a humidifier and, despite what they say, a TEENY TINY dab of Vicks not ON HIM, but on something he's wearing, etc. Humidifier(s) in his room make a world of difference and if you haven't been suctioning his nose, start. He'll hate it, and so will you (Ethan's 14 mos and STILL hates it!) but it has to be done sometimes. But I had the same problem and I kept thinking, "Is it colic?? What am I doing wrong??" I found a great pediatrician, though, and they determined acid reflux.
if the pedi hasn't tried an acid med, it can't hurt to demand it; and you can buy Prevacid at the store to see if it helps. It can't hurt him. Ethan was put on 7.5mg at 2 months and about 6 lbs and he's still on that dose, and that's half a 15mg tablet; he takes the dissolvable ones and now I just give it to him like a Cheerio, and it's as easy as pie.
Oh, and you can give him a little bit of Maalox. See if that doesn't help! Give him about as much as you get when you buy infant Tylenol and you get that dropper that comes w/ it - fill that size dropper with Maalox and see what results you get.