So what's the native Chinese greeting? It's a simple "Ni Hao!" (你好!). Why do the Chinese people not like to append a "Ma" (吗)? I don't know. Whoever invented "Ni Hao", perhaps during the Vernacular Chinese Movement a hundred years ago, probably didn't like to make this frequent greeting phrase any longer than necessary.
If you do need to ask the question as if saying How's your situation?, "Ni Hao Ma?" certainly makes sense. That is, this 3-character question is used in an inquiry, not greeting. But in that case, "Ni Hai Hao Ma?" (你还好吗?) or "Ni Zuijin Zenme Yang?" (你最近怎么样？) may be just as or even more common. Similarly, you ask the plural "you" with "Ni Men Hai Hao Ma?" (你们还好吗?) or "Ni Men Dou Hai Hao Ma?" (你们都还好吗?).
[2012-06 Update] A Taiwanese pointed out to me that "Ni Hao Ma?" is said among Taiwanese. I don't recall hearing them say that in a greeting; I can't imagine two native Chinese/Taiwanese walking toward each other and both saying "Ni Hao Ma?" to each other, shaking hands. But it may be because I haven't had enough greetings with them. If "Ni Hao Ma?" is more common among Taiwanese and "Ni Hao" more common among the mainlanders, again, in greeting, not inquiry, then this posting may be titled something like "Ni Hao Ma?" is not a native mainland Chinese greeting. (After all, there's not one single Chinese linguistic authority in the world, but as many as the number of regions where the majority of the population speak Chinese.)
[2013-05 Update] In case a reader is still confused, I'd like to briefly emphasize the main point: The single Chinese word "问候" has two meanings, greeting and inquiry. In the sense of greeting, "你好!" is the choice. In the sense of inquiry, "你好吗?" is a perfect question sentence. This short note is about greeting, as when two friends run into each other on the street and neither had any recent incident that would worry the other. Saying "你好吗?" as a greeting sounds foreign, or causes confusion or misunderstanding.