My daughter had similar trouble when she began junior high and into high school– mostly because her elementary friends peeled off for one reason or another. She was unhappy. Last year I started her in a private school (almost by accident), and I was completely surprised by her willingness to visit the school. I’m a big proponent of public education, but for her the tight-knit, welcoming community was an immense improvement. You might look around your area and see what’s available. Some of them are religious (not a bad thing sometimes :)), but not all are religious, and in our case there was a sliding scale based in income. Still is expensive, but I consider it the best money I’ve spent in the last decade.
Good Luck to you and your Son and keep the faith that things will become easier for him!