This is a much different boss battle than one is accustomed to in the Zelda World. You control Link on the bottom screen but you cannot see Crayk. The top screen shows the first person view of Crayk. You can actually see what Crayk sees as he is stalking his prey.
Crayk's main form of attack is when he gets close to Link, he picks him up and shakes him. A sign will pop up on the bottom screen telling you to rub. Just rub your stylus back and forth quickly in order to shake yourself free from his claws. Link's health will drain more the longer he is in Crayk's grasps.
There are also little Crayklings that are all around the boss arena. They crawl around the floor and really don't have any attacks at all. They will only hurt Link if they come into contact with him. Link can defeat these enemies if he'd like to get some recovery hearts as well as some Arrows.
In order to defeat this first phase of Crayk, Link must use the combination of the bottom and top screens on the DS. When you can see yourself through Crayk's first person vision. Equip your bow and aim right at the camera, which in this case is Crayk's vision. Line up the Bow perfectly and then shoot an arrow. This will make Crayk visible and stun him for a few seconds. Run on over to him and slash away at his large body with your sword, slowly cracking it's shell back.
Be careful and try not to get too close when you are striking Crayk down, as Link will take damage if he touches Crayk. After stunning him several times and striking at him with your sword, his shell on his back will shatter, leaving just its skinny body.
He no longer is invisible and this portion of the battle is considerably easier. All you need to do is strike him right in the face and he will cover up, trying to protect himself. When doing so, he will not move for a few seconds, which gives you some time to quickly run around him and strike him in its blue weak spot. It does not take many hits at all to defeat Crayk. Just keep repeating this process until he is finished.
The player is rewarded with a Heart Container.