By the "Sea Side Cave" I assume you mean the Sea Spirit Cave. You can get one of the legendary birds (Articuno, Zapdos, Moltres) there in the post-game. Look here for how to do that.
The other two locations don't have the Legendary Pokemon. Instead they both have Mega Stones if you are there between 8 - 9 PM in the post-game (once you have upgraded your mega ring). The Chamber of Emptiness (I assume that's what you mean by the "cave of emptiness") has a Banettite and the bottom of Reflection Cave has an Alakazite.