He finished 54 holes at 15-under-par 201.
Henrik Bjornstad (67), Stephen Gangluff (68) and Nicholas Thompson (69) share second place at 14-under-par 202. Aron Price carded a 2-under 70 on Saturday and is alone in fifth place at minus-13.
Whittaker parred his first four holes in the third round, then recorded back-to-back birdies from the fifth. He parred out to make the turn in 34 and was very much in the hunt.
He opened his second nine with a birdie at the 10th. Whittaker parred his next three and birdied the par-5 14th to reach 15 under par and take the lead in the championship.
Whittaker dropped a shot at the par-3 17th to fall out of solo first. He drove into a fairway bunker at the par-5 closing hole, but managed to make birdie and reclaim the lead.
Whittaker is in the middle of a hot streak. He is 27th on the money list, but last week lost to Brad Adamonis in a playoff at the WNB Classic.
'I'm playing good, and it's been like that for the last six or seven weeks, starting in Omaha,' Whittaker said. 'I knew I was playing good coming into this week. After the playoff last week, I wasn't too disappointed because I had a good chance to win and just didn't. I can't dwell on it. I just have to get things done tomorrow.'
Overnight co-leader Scott Sterling only managed a 1-over 73 on Saturday. He is tied for sixth place with Martin Laird (65), Patrick Sheehan (67), Esteban Toledo (67) and David McKenzie (69) at minus-12.
Tag Ridings, the other second-round leader, shot a 2-over 74 and fell into a tie for 11th at 11-under 205.