Do you need a library with a JNI wrapper or just a native one?
We are using FFMPEG (libav) for that purpose, but it doesn't have any ready to use JNI. You can search for a Java wrapper though.
It's quite heavy weight, but can do many various stuff. The cons are that there isn't much documentation in the internet. And almost all tutorials are now outdated because the API changes really fast.
That's a good tutorial to start. The best documentation is their doxygen at http://ffmpeg.org/doxygen/trunk/index.html or http://libav.org/doxygen/master/
We haven't found anything better yet..