You could
- select a part of the website
- drag it onto DEVONthink’s icon in the dock
(this creates a webarchive of the selected part) - convert the webarchive to PDF
(Data > Convert > to paginated PDF)
There’s also a Smart Rule script which moves a webarchive into the current group and selects it so one can see whether everythings fine. If you’re capturing a lot webarchives that’s a very comfortable way as you don’t need to select the destination group each time and the result can be checked without switching between Safari and DEVONthink.