Georg Cantor was a German mathematician who created set theory that has become a fundamental theory in mathematics. However, his original work on infinity and ordinal number was considered unconventional or even unorthodox, which was under heavy attacks from some of the famous contemporary mathematicians for a long time.
Another example is Charles Sanders Pierce, an American philosopher and logician who made important contributions to logic, relation theory, pragmatism, semiotics and so on. But his work was largely ignored in his lifetime and he could not even find an academic position. Only since 1920s, his original work has been rediscovered and he is recognized as one of the most original and versatile of American philosophers and America's greatest logicians.