I honestly hope that nothing comes out of his boss playing with him (although she probably will cause problems when MC decides to not dote her with his attention). And I feel like the intern has a simple crush while Sayu has genuine feelings budding for him. Which is to say that I don't think he should get together with either of the three, as it stands right now.
First of all, he needs to grow a pair. Giving his boss green lights to lead him along just isn't the way to go.
Second, his intern is too obvious, even though he is oblivious. The reason I am against her is her "cute klutz" attitude to get them interacting and what she said this chapter. Sure, they know there wasn't anything more, but especially after knowing that he confessed to his boss, you just don't say that where anyone (especially her) could overhear. That's just asking for misunderstandings.
Thirdly, Sayu. They are good for each-other and will definitely grow from their current arrangement. What I am worried about is what will happen when they realize their own feelings for the other. Because there certainly is something budding there, and the MC is not viewing himself purely as her guardian anymore. He tries his best to leave it at that and I respect that deeply. But it won't stay at that. And even if they do confess, I feel like he will try to push her away, hurting them both. Something has to change in their relationship before that can go smoothly in any direction.
Not mentioning his boss will freak out when he does end up having a girlfriend. Which might happen without him trying to push Sayu away as he might soften up to his trainee. The actual worst case scenario, honestly. If it were his thot boss, Sayu would be hurt but live with it as she was first and the klutz would probably leave the company. Not ideal either, but "choosing" the intern would cause an outrage of the other two. His intern would accept the pure and (honestly) altruistic start with Sayu while thot patrol would have their hands full with his boss. Whom he needs to put down with clear words before the time comes. She just needs to learn that she cannot expect people to always admire her for her body if all she does is keeping them on the line with the occasional tease. The MC needs to learn that too before he enters a relationship with either the intern or Sayu.
Finally, while she is underage I do think that Sayu is the best choice for the MC. After more character development. And maybe two years having passed.