I don't know about any Freeware app that might do the work.
I can recommend using Macromedia Dreamweaver for that kind of job. But if you go with Dreamweaver, do some tutorials, etc. to get the feel of Dreamweaver, as it is not so easy to use (for creating Dynamic websites). But its still the best!
The hard part is going to be getting an app that can interface with your site and create the pdf. You may be able to feed it to one of the pdf printers out there from a more generic format.