The genetic data is clear that interbreeding took place, and neanderthals contribute a few % of modern human DNA in many Eurasian populations. The lack of surviving neanderthal y chromosomes could be suggestive of genocide though, but it's also possible that the neanderthal y chromosome lineages in humans disappeared due to subsequent expansions by newer lineages in human populations.

For an example of non-genocide, look at African bushmen. While their relations with other humans aren't always great, African bushmen populations haven't really experienced any genocidal decline. But if/when they fully interbreed with other humans and get incorporated into the gene pool (after evolving as a separate branch from mainline homo sapiens for over a hundred thousand years), their genes will be an even smaller fraction of the human gene pool than the neanderthal genes.