For STEM fields, is there self-segregation in United States academia?
There probably is some self-segregation, but nothing above what people normally do in everyday society.

I think it's worth keeping in mind that much of the dialogue regarding segregation deals with the actions of government, an extremely powerful 3rd party. Self-segregation is at best an ethical issue, not legal. Moreover, everyone has a right to free association and can decide who they want to deal with.

Arguably, I would say that academia self-segregates less than society at large, due to more liberal attitudes of academics and students.