Well, that would depend.
Usually a Pokemon caught in a Poke Ball has been caught at a lower level than another Pokemon of the same species caught in an Ultra Ball. Because of this, the former would have more EVs than the latter, and thus would be a little bit stronger. Of course this isn't always the case: sometimes a Pokemon is caught with an Ultra Ball or other Poke Ball at a low level because you ran out of Poke Balls.
Other than the above reasoning, there simply is little to no validity to your claim. Some Pokemon are just stronger than others. The kind of Poke Ball used to capture them has no impact on them whatsoever. Seriously, you can capture two Zapdos - one with a Poke Ball, and one with a Master Ball- and each one would have an equal shot at defeating the other. Especially if caught at the same level. :\