In the state of New York, NPR is heard in the state's biggest markets on stations which began life as commercial AM or FM stations and were then purchased by community-based not for profit organizations.
In New York City, WNYC AM & FM (830/93.9) and WQXR (105.9) are on commercial frequencies; the 830 license began as a commercial daytimer on 810 in the 1920s, the 93.9 was a commercial frequency built from scratch by WNYC when no one wanted FM licenses in the 40s, and 105.9 was a commercial station until about three years ago. In Buffalo, WNED AM & FM (970/94.5) were commercial WEBR AM/FM until 1976, and in Rochester, the NPR affiliate is WXXI-AM 1370, formerly WSAY and formerly the property of the Lew Dickey family of Cumulus fame until 1984--it was one of the first stations that formed the nucleus of Cumulus along with Toledo's WOHO-AM.
In each case, they were struggling commercial stations which found greater success as community-owned noncomms.