A good case can be made that Kushner's screenplay shouldn't be eligible for the "Best Adapted" category because it wasn't really "adapted" from anything. Kushner has made clear in interviews that he did quite a bit of independent research in preparing his script--enough so that the logical category to nominate it for would be "Best Original Screenplay." Goodwin probably helped him do the research; apparently she was involved in the project after the rights were purchased. So perhaps the screenplay credit should be "based in part on help from Doris Kearns Goodwin."
But that begs the question of what, if not Team of Rivals, is Lincoln's principal source. The answer is almost certainly Michael Vorenberg's Final Freedom: The Civil War, The Abolition of Slavery, and the Thirteenth Amendment, first published by Cambridge University Press in 2001. Vorenberg's book (which I made my TNR "best book of 2012" pick) is widely recognized as the definitive history of the political machinations involved in passing the 13th Amendment, a subject that received scant attention prior to publication of Vorenberg's book because most historians have tended to focus instead on the Emancipation Proclamation. Lincoln is known, after all, as the Great Emancipator, not the Great Manipulator of Congress Into Codifying the Executive-Branch Freeing of Slaves, Which Only Ever Applied To Confederate States, In A Constitutional Amendment That, After Lincoln's Death, Still Required Passage In State Legislatures. Vorenberg (who, incidentally, is an associate professor of history at Brown) writes in his introduction: