To my knowledge (and feel free to correct me if I'm wrong), the only mutant Mister Sinister has killed with his own hands is Malice, the former leader of the Marauders, who he disposed of in X-Factor 105. Human casualities include Toby Rails & the Bogarts (Classic X-Men #41 & #42 BU, respectively), both parties involved in the life of Scott Summers.
However, Sinister was the mastermind behind the infamous Morlock Massacre, and if that wasn't bad enough, he can be indirectly blamed for the release of the Legacy Virus, which has taken countless mutant lifes, sometimes even important ones. His Age of Apocalypse counterpart was just as willing to spill blood, killing Nate Grey's friends Brute and later Forge (X-Man #2 and #3, respectively), the latter death driving Nate to kill Sinister himself.
So, in summary, Sinister's killed quite a few people. Remember, those are just the ones we KNOW about.
And for Nataku: while Sinister and Apocalypse may seem similar, in truth they have very different powers. Apocalypse is a born-mutant with the power to alter the atomic structure of his body at will in order to change his form, increase his size, and / or give himself virtually any superhuman physical power. Sinister on the other is a human modified by the technology at Apocalypse's disposal, and he does not possess any of the powers of 'Poccy save his immortality and ability to shapeshift. From what we have seen, Sinister's regenerative capabilties are superior to those of 'Poccy, and Sinister also possesses the ability to 'shut down' a mutant's powers, as seen in X-Man 18-19. It should be noted that both Sinister and Apocalypse's "costumes" are in truth extensions of their bodies, which they can alter at will.