According to the Capcom team in the game's official Japanese guide book, they were asked about the meaning behind the name of Ibis island, and they responded:

"The name of the ibis bird in Japanese is “toki” (a homonym for time), and we liked how that word resonated with the game’s themes of “extinction” and “time”… we could probably come up with a number of different explanations for the name, but basically we liked those associations. Also, considering the name of “Raccoon City” from Resident Evil, maybe there’s a lot of animal lovers on the team too."
Contributed by ProtoSnake