The Xindi might be everywhere, really. Their culture consisted of multiple species, was governed in a somewhat repressive manner, and (largely for the latter reason) managed to remain ignorant of the existence of at least one further, now extinct species. Several other "member species" might have been discovered later on, accounting for the Xindi Starbase of "The Battle" and for the Feline Xindi of "Slaver Weapon" etc.
On the other hand, whatever killed the Avian Xindi might have been built in to the entire spectrum of species originating from their birthworld - or related to the Sphere Builder designs on the culture. Perhaps the species died off one by one soon after the Delphic Expanse was dissipated?
Or perhaps whatever need or will or sentiment connected the different species originally was removed by Archer's antics, and the species still exist, but none of them call themselves Xindi any more. Any of the named but not shown species of TOS, TNG or DS9 could have formerly been part of the Xindi culture, but would now go by a different name.