MiKTeX 2.9 comes with both and they apparently do the same thing. I was wondering what the difference between them is (if any) and which one is preferable for large documents.
Two things that come to my mind:
Latexmk requires Perl while texify is a native command line application.
texify can trigger the automatic-download for missing packages. I’m not sure if latexmk can trigger it too.
And as TeXworks is available within MiKTeX you have another option, although its focus is not the same as for texify or latexmk.