The world number one set the pace in the morning wave with an impressive round consisting of six birdies, an eagle and two bogeys to lead by one over former Open champion Louis Oosthuizen.
South African Oosthuizen matched McIlroy's 65 to move to 11-under 131 at the FedEx Cup playoff event while Woods and fellow American Ryan Moore shared third at 10-under 132.
"I'm very pleased with how I played today, how I played yesterday as well, and I'm in a great position," McIlroy said. "I got off to a nice start and just kept the momentum going.
"Everything seemed to work pretty well out there. I felt like I drove the ball a bit better today and hit more fairways, which gave me some more opportunities to make birdies, and I was putting well enough to take a few of those."
McIlroy finished nine shots behind Barclays Classic winner Nick Watney in week one of the playoffs in his first appearance after claiming the US PGA Championship.
The 23-year-old was unperturbed, however, suggesting the greens in New York were not entirely up to scratch and he just needed to shake a little rust off his putter.
He leads the field in strokes gained putting and total putts after the opening two rounds.
"There's been a big improvement in my putting from last week to this week," he confirmed.
"I wasn't very comfortable on the greens at all last week. They weren't the best surfaces. I think everyone saw that.
"This week the surfaces are much better, and it gives you a little more confidence that you can roll your putts at the hole a bit more."
Woods had the opposite problem, lamenting a poor day on the greens.
After ranking seventh in the field in strokes gained putting on day one, the 2006 Deutsche Bank champion fell to 68th in the field in round two.
"I'm happy with the way I hit it but I didn't putt very good," Woods said.
"I didn't really make anything. Today was one of those days where I had some good looks, missed them, but didn't feel like I was really rolling it correctly.
"My speed is good, it's just that I need to make a few more. Hopefully tomorrow will be a lot better."
Oosthuizen's round was highlighted by a magical hole out flop shot for eagle from just off the drivable par-four fourth. He added five birdies with just the lone bogey.
"I played really well and I hit the ball nicely," Oosthuizen said.
"Hit a few loose drives out there but gave myself a lot of birdie opportunities."
The playoffs are over for several players who missed the cut, including K.J. Choi and Rory Sabbatini.
The leading 70 players on the FedExCup points list after this event advance to the BMW Championship, with the top 30 then progressing to the Tour Championship finale in Atlanta, where the overall points winner pockets a $10 million bonus.