Use the isoparser library it is as far as I know the only pure Java tool that can mux AAC and H264. It also provides an example for precisely the use case you are describing.
Full disclosure: I am the creator of the library.
AACTrackImpl audio= new AACTrackImpl(new FileInputStream("sample.aac").getChannel());
H264TrackImpl video = new H264TrackImpl(new FileInputStream("sample.h264"));
Movie m = new Movie();
m.addTrack(video);
m.addTrack(audio);
IsoFile out = new DefaultMp4Builder().build(m);
FileOutputStream fos = new FileOutputStream(new File("output.mp4"));
out.getBox(fos.getChannel());
fos.close();