Personally, I would talk to your son about his behaviors that you see as potentially annoying to other kids. If we're at a play area, and I see my son being too touchy, I pull him aside and tell him like it is. Sometimes kids don't like to be touched and if you do that, they might not want to play with you. Then I send him right back out there with a "have fun and go play." Or if he's acting like a goofy, scary monster, scaring or putting off the little girls, I might jokingly tell him they're being 'fraidy cats' and he needs to go easy on them... and he gets it and changes his behavior for the situation. (This just happened yesterday, btw, at the McDonald's play area.) But sometimes he doesn't get it on his own. He needs me to coach him, if you will. I think it's important to let kids know what things are annoying because sometimes, they just think they're trying to engage other children, when in fact, it's backfiring.
I also think there are just some kids who are more sensitive to being accepted. What I mean by that is that there are kids who seem oblivious to the kids around them 'wanting' or 'not wanting' them to play. They just mix right in, and go with the flow, and have no idea that they were wanted there or not. And sometimes, that attitude helps the kids to accept them, kind of like, "well, he's here, so we might as well include him." But some kids are much more keenly aware of being invited or accepted into a group to play. These kids, on even the slightest hint of not being invited into a group, even though in reality, would probably be accepted just fine if they just mixed in, will avoid the situation altogether, rather than risk being rejected. For those kids, it's harder to 'just blend in.'
I'd say to arrange some one-on-one play dates for your son. And use those times to coach him on limiting 'annoying' behaviors... And I'd also continue to build his self-esteem with positive activities, etc., continuing to encourage him to engage with other children, and reassuring him that he's liked and wanted as part of the group.