No, they do not mean the same thing. To kill two birds with one stone, means to achieve two objectives with one action (e.g., by reading A brief History of England, you've both practiced your English reading skills and you've brushed up on your English history). To have the best of both worlds, means to have the advantages of two things that were somehow thought to be mutually exclusive (or at least were thought be quite distinct from one another). So let's say you're using a language textbook that combines modern and traditional pedagogical approaches, if the textbook is able to extract what's really good from each method, you can say it has the best of both worlds.