If we are not including the hiraijin, he is not the fastest ninja. He is still up there, but he is topped by at least Naruto and the TTJs.
If we are counting the hiraijin, than he shares the top spot with the other teleportation space-time jutsu users like Tobirama or Sasuke since the hiraijin/ameno are instant, and you can't go faster than instant.
Well, technically, Minato should be physically fastest anyway, since even Fourth Raikage has needed a bodily boost of Lightning Release Chakra Mode to achieve reflexes comparable to Minato (in base, as it seems). Not to mention Naruto and TTJs use similar bodily boosts (NTCM and Six Paths Senjutsu) and thus beat him in speed only thanks to these enhanced modes.
Yes, i didn't rule out the chakra enhancements, but these are constant states for the users. You can't really portrait Naruto right now without the sage/kyuubi amps specially since the can use them in a snap of finger. If Naruto enters kcm, he will always have that speed through his state. Minato need to have a hiraijin mark placed somewhere to go to that place. It's not quite the same thing. Naruto requires little to no preperation at this point. Minato need to place his mark first. This is why i excluded hirajin but still kept the chakra amps.
But yes, if we are not counting chakra/sage enhanced, Minato is still the fastest ninja ever.
well, Naruto would be the fastest with the vapor release, kaguya, maybe hagorama or hamura (both had physical amps, like tensiegan cm, and ttj, but they had it on a more perfect lvl than anybody else), guy, toneri, momoshiki, madara, obito, minato, sasuke, kinshiki, and the some of the fodder. (im talking bout physical speed, btw)
minato has both physical speed and instant transmission speed. he uses a combination of body flicker and flying thunder god. Ay for example used body flicker and lightning armor. but minato's yellow flash persona is because of the body flicker not his flying thunder god, as there is no flash when he uses it, there is just him disappearing and appearing somewhere else. minato's body flicker alone was just as fast as Ay's he simply amped up his already quick body with flying thunder god.
also Naruto and sasuke were both moving astronomically fast in their final fight.No power ups just raw speed they both had developed by the end of the war.
naruto using six paths senjutsu was so fast that he instantly speed blitzed madara who had previously been able to react to gai's 8 gate speed.