for (CoreMap sentence : document.get(CoreAnnotations.SentencesAnnotation.class)) {
    ...
}

sentence.get(CoreAnnotations.TokensAnnotations.class).remove(token.get(CoreAnnotations.IndexAnnotation.class));
token.setWord("John");
sentence.get(CoreAnnotations.TokensAnnotation.class).add(token.get(CoreAnnotations.IndexAnnotation.class),token);