Hello,
You should be able to publish an RTMP stream to a Wowza Streaming Engine application using FFMPEG. Wowza does support an RTMP stream wrapped as MP4, when using H.264 video and AAC audio codecs.
Here is a forum thead where you can find some frequently used FFMPEG commands with a Wowza server: Frequently requested FFMPEG command examples for Wowza
Zoran