MS Word 2013 will hyphenate polytonic Greek documents even automatically; for older Word versions you can download Ancient Greek Hyphenator, a convenient free template that adds accurate hyphenation macros. I have tried it in a long document (900 pages) written in polytonic (ancient and modern) Greek, and it worked without faults and very fast.
A help file is included in the installation, but there should be a warning about Word’s Index. If you have created an index, after hyphenation all index entries that ‘touch’ a word which can be hyphenated, will be lost. Υou must place index entries to touch a punctuation mark or a small word, a word that will not be hyphenated, like an article. Punctuation marks and empty spaces save the index entries. Experiment with index entries in a selected text before you hyphenate the whole document.
Ancient Greek Hyphenator works also on the 2007 version of Word. Just place it inside the StartUp folder of Word, and you will see a new menu “Add-Ins” which contains the AGH command, to open the Hyphenator options and start hyphenating your document.