The seeds are dry, why get them wet again? Since you've already knocked the seeds loose, just use a sieve or two to get rid of most of the chaff.

Rodney

For my own use, I don't worry about removing all the chaff. I'll take out whatever is easy with screens, winnowing, etc. but the rest gets "planted" with the seeds. The seeds grow fine and the chaff decomposes quickly.

I'd agree not to wet the seeds unless you have to. Usually a screen or colander will get much of the chaff then use a fan and some large plastic containers or buckets to winnow. You should get the seeds mostly clean that way and as naturegirl say's, don't worry about making it perfect.

For all the work you put in to it, I hope the onions weren't hybrids to begin with.

-Mark

Seed to Seed says to just winnow them out dry. I have some embroidery hoops with nylon net I use for this. I also go through and save only the biggest seeds. Good luck!