All said there. AGP runs at 1066MB/s and PCI runs at 133MB/s of I remember correctly...
Oddly enough, some PCI video cards where faster than AGP "back in the day" LOL. Read up on the old Voodoo3 3000. The PCI got the same or higher score on it's tests, or most of them.
But back to the question, there will be quite a difference between them. Never tried newer cards as PCI myself, though... Something to keep in mind, I would suspect 2D graphics would be almost faster with Onboard AGP. Are you upgrading for 3D games, or some 2D graphics?