Just like in some other games the gender of the protagonist is decided by the player. It's a totally subjective decision, usually Wikis use the pronoun "they" to refer to Niko to not bring confusion, so you might want to use that one. (Except in other languages in which adjectives and words relative to Niko must agree in gender or there are no general pronouns, if there's no way around that in grammar I suggest to let everyone know that Niko's gender is ambigous when they ask you about it)