Funk maintained his first-round lead by shooting 8-under-par 64 in Saturday's second round.
His score after 36 holes is a five-year low 15-under 129.
Japan's Kiyoshi Murota, a sponsors invite, is second after shooting 7-under 65.
He is 12-under 132.
"I'd like to be hitting my irons in there a little closer and just keep giving my putter a chance," Funk said about his plans for the final round. "My putter is doing really well right now. It has saved me the first two days."
Veteran Tom Kite (66), the 2003 runner-up, is alone in third place at 11-under 133.