The American was at 201 after firing his third straight 67 at the Plantation Course in Kapalua, Hawaii.
Hideki Matsuyama, who has won four of his last five starts, lurks in second, two back of Thomas.
Matsuyama had his best round of the tournament with a 66, which tied William McGirt for the lowest score of the day.
World No. 1 Jason Day (70) has his work cut out for him as the Australian was in joint-13th at 209.
Thomas finished 21st previous year on his first trip to the annual event at Kapalua, a full 19 shots behind victor Jordan Spieth.
"I am just looking for a chance to win", he said.
A rising star on the Tour, he posted six other top-10 finishes last season.
In Saturday's third round, he fashioned a string of three straight birdies beginning at the par-four third hole.
Walker drained a long-range birdie at the first and Reed picked up a shot at the third to briefly make it a four-way tie at the top, only for Thomas to move ahead with a hat-trick of gains from the third.
On the short 16th, he pounded another drive within 60 yards of the pin, but his wedge came up well short and he missed from 15 feet.
Thomas, who went round in a six-under-par 67, might have been a solo leader had he not bogeyed the par-five 15th, his only blemish of an otherwise fine round.
He is seven shots adrift at five under.
"I'm definitely not disappointed with today, but I left a lot out there", Thomas said.
Defending champion Jordan Spieth had yet another indifferent round, shooting a three-under par 70. He was alone in 19th at 211.