Safari has one of the more in depth cache clearing systems. This is basically how you do it.
Go to the Safari menu, and click on Preferences…
Click on the Advanced cog on the right, then check Show Develop menu in menu bar. Click close button.
Click Develop menu, the click Empty Caches.
From the Safari menu, click Reset Safari.
Typically your going to want to check everything, and then click Reset.
All done. If you have done this in a while it might take a bit, so be patient.