I don't know of a better place to buy it. I didn't realize that EB was selling a d/l-able version.
Infogrames Interactive was the first Publisher of Civ3. Then they bought the Atari name, and between Play The World and Conquests (2003 sometime) they changed their name. So technically it's the same publisher, just with a name change.
So do you have Civ3 on a disc, or was that a download as well?