This is just my opinion. Take it with a grain of salt. I have dealt with a spiteful ex for many years now. I don't feel like you owe her anything. He didn't tell her that he had a girlfriend. In reality it is none of her business. Having his son around a nice female role model is not a bad thing. It would be different if he were taking him to bars with him to pick up chicks and not telling her. If he were acting in ways detrimental to the boys health and well being, she would have a valid complaint. In his defense, he didn't tell her because he didn't want to deal with her wrath. My experience with bitter ex's has been that if you try and be their friends, or apologize or give them an ounce of an upperhand, they will take it and run a mile with it. I would be friendly and cordial. I would not apologize for your existence or because she wasn't included in his decision to have a relationship with you. I also would NEVER tell her that a decision that he made with something do to with her caused you to break up with him. Don't consider yourself the intruder.
I know this sounds harsh, and cold. I know that in your mind that you want it to be one giant, perfect, blended family. And, hopefully you can figure out how to do that. The sad part is, it just isn't that easy. When my husband and I met, I actually thought his exwife and I would be great friends. We talked to each other on the phone, hung out together at sporting events for the kids. I was even comfortable enough for us to move 5 minutes away from her. It wasn't until then that I realized I jumped from the frying pan into the fire. All this time I was befriending her, she was taking things I said and twisting and manipulating them to my husband to cause rifts between us. Luckily, my husband was in tune with me enough to know she was lying. So, I cut off all ties with her, and then she really got nasty. She could no longer manipulate me herself, therefore she had her children do it for her. Which is a much harder dynamic for my husband to see.
I'm not trying to scare you, I just am not sure that I would buddy up to the ex. In time she will see you are a good role model for their son. And if she doesn't, it doesn't really matter. She can't dictate who his father dates. If your bf truely want visitation, go to court and get visitation. His ability to be an active participant in his son's life should never revolve around his new girlfriend. He shouldn't have to prove anything to her. He needs to prove it to the courts.
I don't know if this helps at all. This is just my opinion, and it may not be much, so like I said before take it with a grain of salt.