Lowrie went deep in the first inning to give the Astros a 2-0 lead, and Snyder broke it open in the second, unleashing a long drive to left that landed on the train tracks atop Minute Maid Park's left field wall.
It was the first homer in an Astros uniform for Snyder, who signed with the team as a free agent in January.
J.A. Happ (2-1) collected the victory with 6 1/3 effective innings, holding the Mets to three runs on six hits. He walked three and struck out seven.
Brett Myers picked up his sixth save with a 1-2-3 ninth, allowing Houston to clinch its three-game set with New York.
Jonathon Niese (2-1) lasted three innings for the Mets, allowing five runs on six hits.