One of the best ways to take down Cretaphid is to obtain the magmul weapon. With the magmul armed and ready you stand a great chance of victory. If used properly, can take out two or three eyes at once. Just aim at the center of a group of blue eyes. They must be pretty close to each other for magmul to work its magic. Use your missile launcher to take out the crystal as it is easist to aim with.