Black is present (called substantia nigra, Latin for black substance) in one of the four deep brain nuclei due to the special pigmentation of neuromelanin, present in pigment bearing neurons of the nuclei in the deep part of the brain. This pigment is what colors the skin and hair, and is part of the basal ganglia.
Although the functional nature of neuromelanin is unknown in the brain, the pigment is made from substances including dopamine and norepinephrine, that are essential in brain function. In humans, these nuclei are not pigmented at the time of birth, but develop pigmentation during maturation to adulthood. (Source)