Two ideas, assuming the document is in Word format:
1: If you've got an online tool that will do what you want, copy the file to HTML, post it somewhere, and do your online word count.
2: Do a Find & Replace in Word, replacing spaces with carriage returns (^p). That should get you one word per line. Then copy into Excel, with one column, with one word per row. Do a pivot table with your word column in the row field, and count of word in the data area. That pivot table will get you a count of unique words in the document.