Eakes has a 36-hole score of 11-under 133.
Bruce Vaughn (64) is second at 10-under 134. One of the first-round co-leaders, Scott Hoch (66), is third at 9-under 135. Another first-round co-leader, Craig Stadler (67), is fourth at 8-under 136, and six players share fifth at 5-under 139.
It was a day many players were dissatisfied with the course at Endicott, N.Y., which caused many PGA veterans to skip the tournament when it was the PGA's B.C. Open.
"We had great crowds today and for the pro-am, but something needs to happen to the golf course or I'm worried about what the rest of these guys are going to think after playing a year or two," Stadler said.