The National Council of Teachers of English gives awards to the top nonfiction titles for children, taking into account the accuracy, organization, design, and style of newly published books. You can look at the 2012 winners here.
The National Council for the Social Studies publishes an annual list of notable books for children in the field of social studies.
The National Science Teachers Association offers a list of Outstanding Science Trade Books for Students.
School Library Journal, a popular review source for school librarians, also compiles a list of titles.
For the past forty-five years, The Boston Globe in conjunction with the Horn Book (a review journal for librarians) gives awards to noteworthy books each year, and non-fiction is one category.
Librarian and children’s literature expert Judy Freeman offers her list of the top non-fiction books of the century.
Since 2001 the American Library Association has awarded the Robert F. Sibert Medal for the most distinguished informational book published in the United States in the preceding year.