Do the Naruto ninja actually need air to go into space? I'm thinking of the The Last: Naruto movie, and I remember that the Borg ships were lousy at stealth. If the Naruto ninja can reach the cube, they will easily get to the Queen (If the Star Trek crew can sneak onboard to upload a virus, any ninja can do so).
As for all of the advantage that the Borg has, with two hours prep, they have to locate, find and kill Orochimaru & Kabuto with the first strike. If either of them survive and get Impure World Resurrection up and running, it becomes a much tougher fight for the Borg. It would become a "zombie" war and not a curbstomp.