W. W. Rouse Ball, in his "A Short Account of the History of Mathematics", tells the story, but this is nearly a full century after the event, and can hardly be the first citation. The Dover Publications edition has it on page 417, and for those who haven't read it, here it is:
"Laplace went in state to beg Napoleon to accept a copy of his work, and the following account of the interview is well authenticated, and so characteristic of all the parties involved that I quote it in full. Someone had told Napoleon that the book contained no mention of the name of God; Napoleon, who was fond of putting embarrassing questions, received it with the remark, "M. Laplace, they tell me you have written this large book on the system of the universe, and have never even mentioned its Creator." Laplace, who, though the most supple of politicians, was as stiff as a martyr on every point of his philosophy, drew himself up and answered bluntly, "Je n'avais pas besoin de cette hypoth\ese-l\a." Napoleon, greatly amused, told this to Lagrange, who exclaimed, "Ah! c'est un belle hypoth\ese; c_)a explique beaucoup de choses."
I have been unable to find any source in the text for this quote, alas. Rouse Ball remarks that "An analysis of the contents is given in the _English Cyclopaedia_." Maybe that work cites the story, and provides a reference?