As of May 2015, Android Studio support for NDK has significantly improved. You can choose between automatic native lib generation, or using your own Android.mk in more complex cases. But AS still does not provide a way to debug native parts of an app (if you are using JNI). This may be the last reason to keep Eclipse on one's desktop.
Update, a year later: Android Studio 2.2.1 provides decent NDK support, and is almost fully compatible with the old Android.mk - based configuration. And it does support C++ debug, much easier than Eclipse ever did.
