Your Ex is an adult, and has been the parent of the 16yr old, exactly the same as you have.
He has had 16 yrs of opportunities to forge a loving and reciprocal bond with his son.
It's simply NOT your 'problem' to solve, it's HIS !
Simply tell your 16yr old that his Dad won't be coming into your home any more as it's inappropriate, so can he please reply to his Dad if he texts or calls, even if it's just to say 'I don't want to see you'.
Then send Ex a text saying that you have told your DS that he won't be able to see him at handovers etc any more so your son is fully aware of this.
And that going forwards, it's up to HIM to work out how/when he sees his 16yr old son, and you won't be discussing it, or involved in this, any further. (Nor will you be passing any messages between Ex and 16yr old, cos that would be his next 'task' for you, trying to make you a go-between)
Big girl pants on, send text, and breathe...
You have said you're worried about the 'fall out' from this (i.e enforcing a basic boundary for your own safety and mental health !), but if he shouts and yells, or throws ALL his toys out of his pram, SO WHAT?? Who actually CARES? You don't live with him. He can take his nasty controlling temper out on his new GF if he likes, that's no skin off your nose!
Actually, you should view any and all 'temper tantrums' as exactly that, a CHILD'S bloody tantrum! And YOU are NOT his bloody MOTHER ! So it's not up to YOU to 'manage' anything for him any more!!
YOU, my lovely, are FREE ! Remember that !