Oh god. wkhtmltopdf sucks on so many levels, Webkit itself being one of them as their fork is totally outdated... sometimes I really think about rewriting it using Chromium Embedded Framework.
I found there is no python API of this feature, so I wrote it, this lib is based on ruby pdfkit
You're better off using PhantomJS to take screenshots.
There's still no great solution for Flash if you have to support that. I did a lot of research on this previously.