 After retiring as an active player, Niemann became a coach and instructor in the New York Mets' organization for over two decades, serving as a minor league instructor (1988–96; 2000; 2003–08; 2011) and the club's Major League bullpen coach (1997–99; 2001–02; 2009–10).Among the managers he worked for was Bobby Valentine, and in 2012 he left the Mets' organization to serve under Valentine and pitching coach Bob McClure as the assistant pitching coach of the Boston Red Sox.On August 20, 2012, he was named Boston's head pitching coach and served through the end of the season, but was not retained by Valentine's successor, John Farrell.