I haven't used this tool but it looks like it should do what you are trying to do:
http://www.transabacus.com/ TransAbacus gets a website address or URL and returns the list of pages on the site, with the number of words for each one. Optionally, the user can also get the number of words in title, alt text and meta-tags (whose translation is as important as the body translation because several search engines use them to accurately index the web page, but unfortunatly they are generally not considered at estimation time). Additionally, TransAbacus counts the words in text files linked by the URL (the current version of TransAbacus counts the words for .pdf, .txt and .rtf files).
P.S. The only downside is that this is a software tool installed on your machine rather then an online service.
Another one that looks interesting is:
http://www.inspyder.com/products/InSite/Website-Word-Count.aspx Use Inspyder InSite to quickly get the word counts of virtually any website. No more "copy and pasting" page after page into Microsoft Word. Now you can word count an entire website with a few clicks of your mouse!
InSite provides a variety of word count information, including total words on site, total words per page, total unique words and totals for each individual word. InSite allow you to save your word counts to PDF or Excel.