One of the hardest things about dating someone with kids and a prior relationship is that you have to share. One of the other hardest things is that some people don't juggle various relationships well in a group situation.
If I understand you correctly, your bf, his son's mom, and your bf's ex (who came after the mom but before you) were all there. Pictures were taken with everyone except you. If I have this wrong, then my answer may be off.
I guess I'd prioritize. The most natural and correct thing is that there were photos of Dad, Mom, kid and some uncles in various combinations. These people have been together since before the child was born, and he has known them all forever. That all makes sense. And not posting the pics on his own FB page? It's typical of teens who only want "cool" stuff on their own pages but still kind of want to share things with their dad. Sending photos from someone else's camera/phone is somehow an extra step to them, so they post directly to the parents' pages. ("Okay, here are the photos I'm pretending I'm not interested in but I know they matter to you.") I know you don't want the mom's photo on your bf's page, but that's what you have to let go of. Everyone who knows him knows he has a son, right? And they know that a woman was involved in making that possible, whether they know her or not (newer friends might not). If your bf has his own relatives (siblings, aunts, uncles, parents) who might want to see how the kid turned out, it's appropriate that they see the mom and that divorced/split-up people can at least be civil at these events.
I'm not sure why the 2nd ex was there, but if she was a friend of the family in some other way, or if she was married to your bf or otherwise in the child's life (especially if she was living with your bf and having his son there on weekends), then they have a relationship. If the boy's mother and your bf can stand having her there, then it should be okay with you.
What's baffling and inexcusable and where you should be hurt is if no pictures were taken with you in them. If you've been with him for 3 years and you were invited to the graduation because you have been a part of this boy's life, then you should have been in some photos with bf and son. (If there's distraction at an event, it's okay to say to one of the uncles or other adults, "How about I take some pictures of you with bf and son, and then you take a couple of me with them?" People sometimes lose track of what's been taken. But if you've been shuttled off to the side, not introduced to everyone, or just designated as the photo taker and not a significant other after 3 years, then that's a huge red flag.)
Your bf should be proud of enough of you to post those photos on his page. Whether he puts them on the son's page is something else again, since the son isn't putting up any photos and since he might not want to explain all of these women (mom, ex, you) to his friends. If you are not in any photos, that's wrong. Your problem is with your bf though, and not with his son. So I would have a good, solid, sit-down discussion with him about where you fit in his life. If he won't do this, get counseling. It can't be about jealousy of other women - you should have been in some photos even if those other women weren't in the picture. If you aren't significant enough for that, then you have a good idea of where you stand in his life, and I'd end the relationship if counseling doesn't change things.