Hi N.,
Either he's just not used to it, since you've always had him sleeping upright, or he has something medical going on like acid reflux (or some combination, perhaps).
Whichever reason is causing your baby to be uncomfortable, you might find that an incline works for him---just be sure to get one with raised side walls so that he doesn't roll off. We used an incline with our baby boy, combined with swaddling, when he was little (now he's 16 months old) and it worked really well---especially since we didn't feel comfortable putting him on his stomach that early.
What's nice is that you can use the incline to put him to sleep on either his back or his side...just adjust those side walls that I mentioned before so that he is kept snuggly on his side and doesn't roll off (ours came with velcro, so that you could narrow or widen the sides). Since the side position is also recommended by the AAP for SIDS prevention, and since it also may help him transition to his back and/or help him with acid reflux, if he has that problem, you may want to try that position in the incline.
One other thing you might try, if the incline device is not a sharp enough incline for him at this first step (you may need to transition him from sharper to flatter incline over time), is to roll up a towel or blanket or place a pillow UNDER his crib mattress to jack up one side and created a sharper incline. Our doctor told us to do that at one point when our baby was sick because it could help with congestion/drainage.
I hope this helps. Good luck!
D.