Apparently Gell-Mann himself prefered it to be pronounced "kwork". However the line it comes from in Finnegan's Wake is "three quarks for Muster Mark" which to me suggests "kwark" makes more sense. G-M thought "quark" rhymed with "quart" as a weak pun on quarts of beer.
But everyone says "kwark" and no one apart from Gell-Mann has actually read Finegan's Wake