They are pretty much synonyms. I see that m-w.com lists each as a synonym for the other.
TO ME, "excerpt" SUGGESTS a long passage that is intended to be read, possibly for enjoyment, as a coherent whole. An example would be an entire book chapter--for example, a whole chapter of a new book published in a magazine.
TO ME, an "extract" is usually shorter than an "excerpt" but longer than a "quotation."