The best tool for the purpose is likely to be FFmpeg.
Download that flv, then convert it with FFmpeg.
If you want to have the best FFmpeg available, you can compile the latest version:
HOWTO: Install and use the latest FFmpeg and x264http://ubuntuforums.org/showthread.php?t=786095
The exact options, you may find in this way.
Type on Terminal:
The option -sameq (same video quality) was always good for me.
The best place to ask questions about FFmpeg seems to be "Ubuntu Multimedia Production Forum".
EDIT: some examples of FFmpeg usage are here:
Linux by Example: extract audio from video or online streamhttp://linux.byexamples.com/archives/22 ... ne-stream/