This is what works for me:
buildscript {
    repositories {
        mavenCentral()
    }
    dependencies {
        classpath 'com.android.tools.build:gradle:0.5.+'
    }
}
apply plugin: 'android'
configurations {
    apt
}
repositories {
    mavenRepo url: 'https://oss.sonatype.org/content/repositories/snapshots/'
}
ext.androidAnnotationsVersion = '3.0-SNAPSHOT';
dependencies {
    compile 'com.android.support:support-v4:18.0.+'
    apt "org.androidannotations:androidannotations:$ext.androidAnnotationsVersion"
    compile "org.androidannotations:androidannotations-api:$ext.androidAnnotationsVersion"
}
android {
    compileSdkVersion 18
    buildToolsVersion "17.0.0"
    defaultConfig {
        minSdkVersion 7
        targetSdkVersion 18
    }
}
android.applicationVariants.all { variant ->
    ext.aptOutput = file("${project.buildDir}/source/apt_generated/${variant.dirName}")
    ext.aptOutput.mkdirs()
    variant.javaCompile.options.compilerArgs += [
            '-processorpath', configurations.apt.asPath,
            '-AandroidManifestFile=' + variant.processResources.manifestFile,
            '-s', ext.aptOutput
    ]
}
After that I need to mark build/sources/apt-generated/debug as source in Android Studio by right clicking it and selecting Mark Directory as > Source Root