My first instinct is to agree with Cindy and Beth, but it is difficult because we don't know the whole story.
I think the most important thing is that your ex has demonstrated that he loves your son as much as if he were a biological parent, and wants to have a relationship with him. I think that kids can't have too many people loving them.
I think that what your ex is doing with the choice he's given you makes sense, if I understand correctly what you've written. Your ex is saying that if the boy doesn't want a relationship with him, and you support your son in that (he's 3- not old enough to make that decision!) then your ex wants to establish with the court the fact that he is not the bio dad. This makes absolute sense because it releases him from obligations that he really shouldn't have, particularly if he's not allowed to have a relationship with the boy. I think it's good and remarkably honorable that your ex is willing to accept parental responsibility provided that he can have a parental relationship, and perfectly appropriate that he should challenge the legal relationship if the parental relationship is denied.
To the commenter who suggested you should get the ex out of your life and focus on the relationship with the new husband: I can't be certain, but from what you've written it appears that your ex is your daughter's dad. That means you can't get him out of your lives. I think it would be best to support his relationship with both your children. I'll say it again: kids can't have too many people loving them. At the same time, you ought to consider having a discussion with both your kids about the many different types of families, and about how there are "biological relationships" and adoptive relationships, defined by love. If your son continues to have a relationship with your ex, it's probably in everyone's best interest to be honest early on about the biological relationships. (Make sure you discuss this with your ex.)
Good luck!
PS, to the commenters who are saying you should listen to the 3 yr old because 3 yr olds are smart or some such rubbish... that's rubbish. 3 yr olds will have tantrums about anything. We all know that 3 yr olds will often have a tantrum because they want something that's not good for them. You need to decide what's best for your son, don't let him decide at that age!