While in New York, Ellis was involved with several Third Stream projects. A live performance from February 8, 1964, at the Lincoln Center was filmed for Leonard Bernstein's "Young People's Concerts" series. He performed with other jazz musicians alongside the New York Philharmonic on Larry Austin's "Improvisations for Orchestra and Jazz Soloists" (1961) and Gunther Schuller's "Journey Into Jazz" (1962). A later recording of Austin's piece, featuring Ellis, bassist Barre Phillips, drummer Joe Cocuzzo, and the New York Philharmonic (directed by Bernstein) was released on an album entitled "Leonard Bernstein Conducts Music Of Our Time" (1965).