After resigning from the Shaar Hashomayim, he served as Director of Research of the YIVO Institute in New York City (1992–1999), which holds the world's largest Yiddish and Holocaust Archives and Library.
Also while at YIVO, Nadler led international Jewish efforts to repatriate libraries, archives and Torah scrolls in Lithuania that had been plundered and confiscated by the Nazis, and later held by Soviet authorities.
His criticisms of Schneerson in The New York Times, and his subsequent negative assessment of Lubavitch Messianism in a series of articles for The New Republic, were denounced by many Orthodox Canadian and American Rabbis.
His evolving theological and historical perspectives, evident in his writings, were however the major reason for his having turned away from Orthodox Judaism, as he articulated in a personal piece in the Baltimore Jewish News.
[3] At the same time, Nadler has published scholarly studies of some of the major sects of Hasidism, such as Satmar, Munkatch and Slonim, in addition to a widely noted analysis of the culinary habits of the Hasidim on the Shabbat and Jewish holidays ("Holy Kugel") was initially been mistaken for and criticized as an anti-Hasidic satire.