Well, if we're breaking out the other supernatural beings... my bet would be on demons unleashed from the very pits of hell. Yeah, nothing quite like a fallen angel to unbalance the competition.

But, no, I'm pretty sure the vamps would have the advantage. Ninja stealth is one thing, but vamps have superhuman sences, including their sence of smell. Of course, gas grenades and flash bombs would throw them off. Vampires CAN be kill through decapatation, so if the ninjas bring along some swords, that would help.

If we had a couple equal-number small armies going against one another, the vamps would lose about half their numbers, but win none the less. In a one-on-one, the vamp would probably win.