I don't really have a strong opinion on who has the strongest arm in the NFL.
I would say that I don't think it's Kaepernick or Ryan.
Kaepernick puts a lot of heat on his throws, but he doesn't tend to release the ball at it's highest point. They almost look like side-arm throws with a flicking motion. On a lot of his deep throws, it looks like the ball is thrown at a low angle so it doesn't stay in the air long enough.
For Ryan, it appears it's the opposite. He doesn't seem to be able to put much heat behind his deep throws, so he throws the football at a high angle. The balls seem to have a lot of air time. The thing is Roddy White and Julio Jones are both able to physically overpower a lot of defensive backs and both are great at snagging jump balls so Ryan has an easier time with deep completions.