Zetts completed 12-of-24 passes for 140 yards with one interception. He linked with Williams on scoring strikes of 44 and 15 yards in the second quarter to give the Penguins (2-1) a 28-0 halftime lead. Williams had four catches for 68 yards and also scored on a 15-yard run.
Smith, who gained 60 yards on 11 carries, scored on runs of 8 and 3 yards. Jabari Scott added 99 yards on 16 carries, scoring on a 1-yard run.
Luke Gaddis kicked field goals of 39 and 47 yards for Stony Brook (2-1).
The Seawolves were hurt by Josh Dudash's four interceptions. Dudash completed 14-of-33 passes for 166 yards but was picked off by De'Angelo Wilson, Myles Banford, James Terry and Dorian Chenault.