Juan Castillo, a 6-foot-5 right-hander making his Double-A debut, worked five innings of six-hit ball to earn the victory for the Mets. Castillo walked one and struck out four.
The Baysox, unbeaten in three outings coming into the game at Binghamton Municipal Stadium, got on the board when first baseman Brent Miller sent an 0-1 fastball from Castillo over the right-field wall with one out in the fourth.
But after Miller's second homer of the season, the Baysox went on to record just two more hits.
The home run created a 1-1 tie, which Binghamton would break in its half of the fourth when catcher Andy Dziadkowiec's sacrifice fly scored Aaron Ledesma, who had reached on a leadoff infield single, stole second and took third Frank Jacobs' single.
The Mets made it 3-1 in the fifth, when Butch Huskey scored from third on a passed ball by Bowie catcher Greg Zaun with two out and the bases loaded.
Denny Harriger pitched a perfect sixth inning and Bryan Rogers a 1-2-3 seventh for the Mets, who had allowed 16 runs in their first two games -- home losses to the Reading Phillies last Thursday and Friday. Binghamton had games postponed because of inclement weather on Saturday, Sunday and Monday.
Baysox starter and loser Kevin Ryan pitched the distance, allowing three runs, two earned, on eight hits and four walks.