The iPod Nano resolution is 320×240.
The iPod Touch and iPhone resolution is 480×320.
Use the following command to convert an FLV file to an MPEG file. That file, then, can be imported into iTunes and converted to MP4 from there.
ffmpeg -i file.flv -s 320x240 file.mpeg
See my page on how to Rip a DVD with FFmpeg for some other conversion examples.
I also have more information about video formats and codecs, ripping home video from a DVD, a story board sketching, and more on my Digital Video page.
There's an online service, http://vixy.net, that will convert FLV files to MP4. It will also fetch YouTube video's and convert those.