Given a choice of the two. Always go with AGP. It's a dedicated port on the mother board that only handles video. (AGP=Advanced Graphics Port)
PCI is the older, more common type.
You may not be able to just go get an AGP card though. It will only work if you have an AGP slot on your Motherboard.
How do you know if you can put an AGP card in your system?
Two easy ways. If you have USB ports on your system and it's not an add on card, (For example, USP ports on the computer case itself) then you probobly have AGP.
The better way,,,
Open up your case and look at your graphics card. If it sits in a slot that looks different from all the others you have AGP. The port looks diofferent because it sits farther from the outside of the computer case, It's likely a different color too.
Go with AGP if you can. It costs the same as PCI cards anymore but it's a better way for your computer to talk to your graphics card.