He has only a slight chance of returning this season.
Team doctor Struan Coleman will perform the procedure at the Hospital for Special Surgery in Manhattan.
Niese departed Tuesday's start against the St. Louis Cardinals after facing only four batters. He arrived with the lingering knee injury in an Aug. 1 trade with the Pittsburgh Pirates for fellow left-hander Antonio Bastardo.
Niese's second tour of duty with the Mets likely will end this offseason. The Mets are unlikely to exercise a $10 million option for 2017.
Robert Gsellman, who replaced Niese against the Cardinals on Tuesday, will take over the rotation spot beginning with Sunday's game against the Philadelphia Phillies at Citi Field, according to manager Terry Collins.
Niese, 29, went 0-1 with an 11.45 ERA in six appearances (two starts) with the Mets this month. The Mets had traded him to Pittsburgh last December for second baseman Neil Walker.