I know some of these aren't skateshops, but they are skater owned:
Rival NYC-Vinny Ponte
Tony Alva-Alva
Tony Ferguson has something to do with Alife Vancouver
Keith Hufnagel-HUF
Nick Tershay is about to open a store
Chris Keefe-Dave's Quality Meats
Kareem Cambell owns a sneakershop in SoCal somewhere...
And Lee Smith doesn't own FTC, Kent Uyehara owns FTC SF.