This fight takes place across the multiverse. While the two of them are hoping across universes with their respective cross dimensional technology, they end up crossing paths. One thing leads to another and before long the two are at each others throats. A scuffle ensues in which both opponents learn that they are dealing with dangerous, technologically capable foes. Each one manages to retreat to their own universe to lick their wounds and plan the next move.
For the sake of this fight, assume that both Stewie and Rick are going all out, even recruiting alternate versions of their respective families as we have seen through different episodes. They have access to their weapons and are willing to call in anyone they can think of to help them remotely win this fight. This in an all out war that will likely leave the multiverse itself shattered. Who wins?