Schuster was recruited to New York University by Kurt Mislow, who was also interested in photochemistry, and joined the faculty there in late 1961 in what was at the time the University Heights, Bronx campus. He remained at NYU for his entire academic career. Schuster received tenure in 1968 and spent the 1968–69 academic year on sabbatical in London in the laboratory of George Porter. In 1974 NYU closed its Bronx campus, requiring Schuster to move his laboratory to the Manhattan campus near Washington Square Park. Among Schuster's influential advisees are structural biologist Dinshaw Patel and synthetic organic chemist Phil Baran, who worked in the laboratory as an NYU undergraduate. Schuster closed his laboratory and retired, assuming professor emeritus status, in 2010.
Schuster was elected a fellow of the American Association for the Advancement of Science in 1992 and received the Arthur C. Cope Scholar Award, given by the American Chemical Society, in 2012.