The best answer is that he was waiting for a Union victory at the battle field.
President Lincoln had first proposed the Emancipation Proclamation to his cabinet secretary in July 1862, but Secretary of State William Seward suggested waiting for a Union victory so that the government could prove that it could enforce the Proclamation.
Although the battle of Antietam resulted in a draw, the Union army was able to drive the Confederates out of Maryland-enough for a "victory" that Lincoln felt comfortable issuing the Emancipation just five days later.