Rotate PDF in Safari
If it's mis-oriented in Safari that means the original is formatted that way. Safari only provides a "quick viewer" of sorts for PDF files and is only rendering what was provided.
What you need to do is open it in Preview.
Simply right click anywhere on the PDF in Safari and select "Open With Preview." Once you're in Preview, you can rotate the PDF with ⌘ CommandL or ⌘ CommandR to rotate left and right respectively.