The Safehavens know for certain that Regice, Regirock, Registeel, Cresselia, and Landorus are dead. Certain other Legendaries have not been seen in a very long time.
Lugia, the Kanto birds, Genesect, Cobalion and Keldeo, and Kyogre are determined to make their presence very known. Groudon, Jirachi, Diancie, and Meloetta sometimes pop up. A dark figure with smoky white hair, and a pink cat with piercing blue and red eyes are occasionally seen, and assumed to be legendaries.
If other Legendaries are alive, and if they are alive where they are, is currently unknown.

yes, grenade launchers, there is no way this can go wrong!