You need to have the discussion with him about the embryo's.
It sounds as though both of you are putting off having a conversation which will lead to a final decision. If you've been working on the marriage for months and it still feels as though he is only living there for your DS, then in all likelihood your marriage really is over, but neither of you have been willing to truly face that.
He may not want to have this conversation because it will mean changes in the amount of time he spends with his son. You might not want to have the conversation because it might mean saying goodbye to your hopes for a second child with him.
But what you're living right now is a kind of limbo - not fair on you, him or your child together.
It's a horribly sad situation but the only way to start to heal is to have that conversation and both of you lay your cards on the table.
It sounds as though the truth is for whatever reason he no longer wants to be married to you. Even if he did agree to a pregnanacy with the embryo's you have to ask yourself - in addition to concerns about siblings having a very different experience of being parented should he not want to be involved - is it fair on your current three year old to go through both his parents divocring and getting used to spending time differently with his mum and dad AND cope with the massive change of seeing mummy having another baby and gaining a sibling.
A new baby is a challenging time. Pregnancy is challenging. Could you really cope with a divorce, pregnanacy, new baby AND supporting your existing child through the heartache of parents separating at once?
I really feel for you, but I think it's time to have a tough conversation and face up to the likelihood that the best thing for all concerned is to divorce and work on building a great co-parenting relationship for your son, rather than adding additional stress to his life via adjusting to a sibling at a time when he will be the most vulnerable he has ever been and life is already very different.