With the appengine-gradle-plugin-1.9.4 there are a few ways to do it.
1: Using the endpoints artifact (this is new) in your project. This requires the appengine project to be part of your android project by specifying it in your settings.gradle file appropriately (http://www.gradle.org/docs/current/userguide/multi_project_builds.html). You can then reference the endpoints artifact from your android project by adding a compile dependency to the build.gradle file (path is a gradle project path, not a file path)
dependencies {
compile project(path: '<appengine-module>', configuration: 'android-endpoints')
}
This will include the endpoints client libraries and their dependencies.
2: appengineEndpointsInstallClientLibs
(installs to local maven repo) which you can then reference in your build file.
3: appengineEndpointsExportClientLibs
while I wouldn't recommend this, if you really wanted to export jar files to a location this would do it.
If you haven't seen the github page, it's worth taking a look to see what you might be able to do : https://github.com/GoogleCloudPlatform/gradle-appengine-plugin