Go to Pacifidlog Town.
Surf east and make sure to keep close to the top of the route, or you might miss the entrance. There is a zig-zagging passage of water that can be passed if not watching carefully.
Once you find the passage, simply Surf north until you come upon the island.
Inside the tower are:
Rayquaza (obviously only one)
Make sure to bring the Mach and not the Acro Bike because you will need the Mach Bike to navigate the falling tiles inside the tower.
You can find maps of the different floors of the Sky Pillar at: