I don't think he's part of any Baptist association. "Baptist" is like "Catholic"; it's not a trademark. Anyone can call themselves a "Baptist pastor".
Phelps is a stooge in the service of, and probably also in the pay of, the loony left. His purpose is to make serious Christians look like freaks in front of the media. The "church" he really belongs to is the church of the far left.
When Phelps' gang protests, they hold gaudy signs designed to offend, walk around, and maybe chant some slogans. They don't sing hymns. They don't pray together. Doesn't sound like any Christian protest I've ever been involved with.
Fred Phelps' church, Westboro Baptist, is an "independent" Baptist church. I don't think this "church" is part of any denomination, or association, or anything like that. No outside religious authority could crack down on Phelps or kick him out - he's already struck out on his own. Frankly, I think Phelps' group is more akin to a cult than a church.