Either way, it doesn't matter much. Samus could just use the Ice Spreader (a large area attack) to freeze his ass and then fucking obliterate him. That doen't work? Use Power Bombs if he gets anywhere near her. He'll be hard-pressed to hit her in ball form because she's a much smaller target and her mobility is much better.

Plus, her lock-on negates a lot of his speed advantages. Meta-Ridley (From Metroid Prime) exhibits the same level of speed as The Ninja does, and she's more than capable of hitting him at a distance. Up close is a bit different, but then there's always the Morph Ball defense.

The big difference between these two is that Samus has an energy shield protecting her suit from any damage. The Ninja relies entirely upon speed to avoid damage, therefore he's at a bit of a disadvantage if he gets hit. He would need to get close to her in order to use his sword, and he would need to slow down a bit in order to use his gun-arm. Either one of those strategies has holes in them, considering I've already mentioned her tactics for both situations. Ninja goes down either way.