Both "most well-known" and "best-known" are completely unambiguous in writing, and mean the same thing. In speech, however, "best-known method" may be heard as "best known method", which instead means "the best of all the methods which are known". Simply for disambiguation while speaking, I would definitely use "most well-known".
In fact, while "better-known" and "best-known" are undoubtedly more common in writing than "more well-known" and "most well-known", as Gustavson's graph indicates, they're both just a little bit more formal than I would hear in everyday usage. Wiktionary lists both forms, but I'm afraid I can't find a more definitive source.