The manga is about ninjas and weren't in real life ninja stronger than samurai?
No. Samurai were highly trained in both armed and unarmed combat: katana, naginata, bow, jujutsu, and pi gua. They were also highly educated and were known to be artists and poets, and adhered to a code of honor.
Ninjas were commonly mercenaries acting as thieves, spies, and assassins that possessed no code of honor; they were dirty fighters that used guerrilla tactics. Hystorically they were likely trained in ninjutsu (in real life, it's not magic) and typically used whatever they could find as a weapon.
Ninjas in the Narutoverse were also confirmed to originally be rogue samurai.
Onoki said that the samurai are very formidable and no ninja village will dare attack them. But, fodder is fodder. The real problem is that, aside from Mifune, there are no samurai that were made to be more than fodder. We can at least infer that fodder Samurais > fodder Ninjas.