If you think about it realistically, Ash's strongest Pokemon should be Charizard. I mean, if you spent the better part of two and a half years (or longer) training your *ss off to get stronger and better your fighting technique, I should think that you'd be pretty strong, too.
But I'm talking as if the anime actually took note of stuff like that. Put simply, the anime phails at realism. You know, what with how Pikachu's strength level magically resets between regions and he nearly gets beaten by a newbie trainer with low-strength pokemon. D:
That said, I don't think Ash really has one pokemon that is "strongest." Doesn't matter if they're freshly-caught or one of his reserves; if you randomly put two of his pokemon against one another, the writers would make their battle look totally epic (or at least evenly-matched) for the sake of coolness.