Oberkfell's specific duties with the Mets have not been announced, while Warthen will replace Peterson as the Mets pitching coach under interim manager Jerry Manuel.
Oberkfell was in his second season with the Zephyrs, having compiled an overall record of 111-105, including taking the Zephyrs to the PCL Playoffs for the first time since 2001 and reaching the PCL Championship Series before falling to the Sacramento RiverCats.
Oberkfell was also recently named the most outstanding professional coach in Louisiana for 2007 by the Allstate Sugar Bowl.
Warthen was in his first season with New Orleans, and has prior Major League coaching experience, having spent 2006 and 2007 as the bullpen coach for the Los Angeles Dodgers.
The new manager and pitching coach for the Zephyrs have not been announced by the Mets at this point.