McGonigle spent most of the 2009 season with the Pulaski Mariners of the Appalachian League. He batted .283 with 43 hits, eight doubles, one triple and two homeruns in 41 games. Against right-handed pitchers, he batted .315. On Aug.17 against Burlington, he went 3-for-4, with a double, three runs, two stolen bases and an RBI. He also appeared in three games for the Mariners of the Arizona League, where he hit .500.

The Houston, Texas, native made his professional debut in 2008 in the Gulf Coast League after being drafted by the New York Mets in the 43rd round. With the GCL Mets, he compiled 33 hits, five doubles, three triples and a .297 batting average in 38 games.  His average improved to .353 (12-for-34) with runners in scoring position. He collected a season-high four hits on July 31 at the GCL Cardinals and drove in three runs on Aug. 4 versus the GCL Marlins.

McGonigle played college baseball for the University of New Orleans, where he batted .294 with 64 hits, 13 doubles, three triples, eight homeruns and 46 RBI as a senior in 2008. In 2007, he hit .258 with 24 hits, 12 runs, two doubles, a homerun and 16 RBI in 31 games. He played for the University of Houston in 2005 and 2006 before transferring to New Orleans.