I don't have the ability to test this, but based on my understanding of the game, I would guess that the projectile receives the damage boost if Mercy is buffing Genji, not the one who fired the projectile.
I'm basing this on the fact that Genji's deflect works by eliminating the enemy projectile and creating a new projectile fired by Genji, this is most obvious when continuously deflecting a Junkrat projectile. You can see that as long as the grenade is deflected, the timer is always reset and the projectile will never explode.
Now confirmed thanks to this Reddit thread.
Genji's Reflected Projectiles: Confirmed! Boosting a Genji as he reflects a projectile WILL increase the damage the target receives. We, unfortunately, did not test to see whether or not boosting the initial source of damage would increase it as well.