Bring 2 cups corn and milk to a simmer in a large saucepan over medium heat; cook 20 minutes, and cool. Pour corn mixture into a blender or food processor; process until smooth. Strain mixture through a sieve over a large bowl. Discard solids. Add salt, pepper, and eggs to corn mixture; stir well with a whisk.
Divide remaining 1 cup corn evenly among 6 (6-ounce) ramekins generously coated with cooking spray, and top each with 1/3 cup corn mixture.
Place the ramekins in a 13 x 9-inch baking pan, and add hot water to pan to a depth of 1 inch. Bake at 350° for 30 minutes or until the center barely moves when the ramekin is touched. Remove the ramekins from pan, and cool for 5 minutes on a wire rack. Invert custards. Garnish with fresh chives, if desired.