Assuming you have not been dosing him with tetracycline, or excessive iron supplements (both of which can cause blackening) it may be you child simply forms such deposits naturally. There are reports that some children are prone to this (different mouth bacteria, diet......) and it typically goes away with time. The are some who suggest that it may even be beneficial since children with the black deposits seem to be far less prone to cavities.

As long as your dentist isn’t worried, I would not be concerned