Theoretically, the question is flawed. Any media (books, comics, movies, television, tabletop/roleplay) that contains science-fiction and especially spaceships, usually have their own conventions and canon. Rather, I should say that one sci-fi author or director will have their own ideas about what is the "fastest" and even "farthest" something can travel. Sometimes the limitation is on speed; sometimes a limitation is upon how far that something can travel before being required (either by dictated space-laws or by technical requirement of electro-mechanical limitations) to stop. A reason for an imposed limitation? Could be for a plot-point in a story; but let's consider reasons.
On the latter point first; more notably, smaller craft like may have limited space for larger/more complex engines to travel further; as much as I loved the original Star Wars trilogy, I always thought it flawed that small craft like X-wings could travel hyperspace -- from an engineering perspective, makes more sense to not have FTL on them, in lieu of using that space for more combat components. (Sigh; I guess, chalk it up to that lore "hundreds of years of republic" of improving technology...)
On the former point, for mandate or "space law". It could be for more general effect of keeping a vessel constrained to a general radius of travel. If you could just fly from one major star system to one at another galactic sector, then the smaller, less-populated star systems in between would rarely receive traffic, and therefore trade activity. (I'd like to think, in Star Wars VI, it makes more sense that the "Rebel Fleet amassing near Sullust" wasn't just one direct hop away from Endor; if it was only one hop away, I'd think ol' Palpy would have been a little less arrogant...)
... In other words, to answer the original question: "the fastest ship in sci-fi" (ignoring the "history" bit) is the one that I have dreamed up, because I imagine being everywhere at once. But knowing that it's unrealistic, I don't write my stories that way, but have a more "realistic" FTL speed in mind...