Android Studio's default support for building NDK doesn't appear to ever work for me. Here's a way to make a build process work.

NDK Build with Android Studio

// add all of these to build.gradle (the one in your app directory, NOT the root of the project)
// to see all files and be able to add your jni directory, you might need to change the view from 'Android' to 'Project' in the file browser

// this goes inside android > defaultConfig (probably after all the other fields eg. versionCode etc)
sourceSets.main {
	jniLibs.srcDir 'src/main/libs'
	jni.srcDirs = [];
}

// these two go at the end of the 'android' block (but still inside it)
tasks.withType(JavaCompile) {
	compileTask -> compileTask.dependsOn ndkBuild
}

// change the path to where you have your android NDK installed
// also change ndk-build.cmd on platforms other than Windows
task ndkBuild(type: Exec) {
	commandLine 'C:\\path\\to\\ndk\\ndk-build.cmd', '-C', file('src/main/jni').absolutePath
}

// that should be it; just change your AndroidManifest to suit your addon (permissions etc, and usually hasCode=false)
// and add your jni directory with native code, Android.mk + Application.mk