To be honest I didn't really understand what you were talking about for a little while because I couldn't believe that you thought he was crying.
I am 94.69% sure that it was just a bit of a failure for the guy animating Ratchet in that scene, it doesn't look like a tear, in fact there were no tears in the entire game, why would they add one (which didn't look much like one at all) for that scene, where he switched from yelling at Clank to talking to Qwark, showing no signs of sadness in his voice.
I'm sorry, but this looks nothing like a tear to me, and I've played the game about 40 something times, without skipping any cinematics, in fact a few times I got bored and just launched through all the cinematics for fun, analyzing them like it was my job to learn every line in the game.