Scii is used with facts, koni with persons.
When the main clause needs another case than the subclause, it is better to put in the other case, too. That would make this sentence:
Mi ne scias tion, kiu li estas.
Now you can see easily, that scias does not refer to a person in this sentence, but to the fact of not knowing.
Easiest would be of course:
Mi ne konas lin. :-)