First of all, "genocide" is a modern concept. There is some scholarly debate whether the Native American deaths count as genocide, since most of those deaths were caused by the unintentional spread of disease. The European/American settlers were pretty damn brutal, but it wasn't as systematic as the Holocaust. Sources

So already, things get fuzzy. But if we try to apply it to historical events, it depends on your definition of "people". If you mean a tribe, then there are tons of examples of 100% (or close to 100%) of the tribe was killed, like the Taino, Caribs, and Arawaks. Basically, a lot of those 90% of Native Americans killed include individual tribes that were 100% killed, and we just don't have any records for a lot of them.

Aboriginal Tasmanians also got pretty close to 100% killed, mostly through disease.

The Moriori were almost wiped out by the Maori.

The Romans exterminated a bunch of smaller tribes around Europe in their conquest. But now, this far back in the past, the line between extermination and assimilation gets fuzzy.

These are just a few examples, but there are probably hundreds or thousands more instances of 100% extermination of tribes, that we just don't have records for. The farther back in time you go, the looser the definition of tribe, the fewer people in a tribe... then the more cases there will be of tribes that were 100% killed, but also the less documentation there will be. History is written by the winners, after all.

Also, this might be stretching it, but the Neanderthals might have been killed off by Homo sapiens (we don't really know).