In my home (I speak Esperanto to my children and am a member of the Akademio de Esperanto), we use biskvito for both "cookie" (or "biscuit" in British English) and "cracker", and kuketo for "muffin", "cupcake" and similar things. The word kekso is a synonym for biskvito.
The word biskvito comes from the *Fundamento de Esperanto", but there its meaning is not very clear, as it is translated into five different languages with words that (at least in modern usage) are not synonyms. For example, the English translation is "biscuit" (which has a different meaning in Britain and the U.S.), while in German it is translated with "Zwieback", a hard twice-baked break (nowadays called biskoto en Esperanto). This probably made some German Esperantists introduce kekso (from the German "Keks") to distinguish cookies from twice-baked bread. The word caught on partially, but biskvito seems to be more common in the meaning of "cookie".