He moved to New York City in 1964, where he came to prominence in the late 1960s as a member of The Free Spirits, an early jazz-rock fusion group that also featured Larry Coryell and Bob Moses.

Their 1969 self-titled sole album spawned the near-hit single "Witchi Tai To" (which received abundant airplay reaching number 69 on the Billboard Hot 100 chart, and on which Pepper was the lead singer).

[1] His "Witchi Tai To" (derived from a peyote song of the Native American Church which he had learned from his grandfather) is the most famous example of his hybrid (jazz/Native American) style; the song has been covered by many other artists including Harpers Bizarre, Ralph Towner (with and without Oregon), Jan Garbarek, Tom Grant, Pete Wyoming Bender, Brewer & Shipley, Larry Smith under the pseudonym of Topo D. Bill,[4] and a version recorded by The Supremes in 1969 that went unreleased until 2022.

In his own projects, Pepper recorded with Don Cherry, Naná Vasconcelos, Collin Walcott, Kenny Werner, John Scofield, Ed Schuller, Hamid Drake, and many others.

[5] He also worked with the Liberation Music Orchestra, Paul Motian' s quintet, Bob Moses, Marty Cook, Mal Waldron, David Friesen, Tony Hymas and Amina Claudine Myers, and toured Europe extensively throughout his career.

[8] With Everything Is Everything With The Free Spirits With Archie James Cavanaugh With Marty Cook With Larry Coryell With The Fugs With Gordon Lee With Charlie Haden With Sandy Hurvitz With Tony Hymas With Paul Motian With Bob Moses With Cam Newton With Ray and the Wolf Gang With Nana Simopoulos With Mal Waldron With Peter Walker With the World Music Orchestra The Encyclopedia of Native Music [University of Arizona Press, 2005], Brian Wright-McLeod