i say intake, if you make it exhaust then the air thats been taken in by the fans at the front of the case will be taken straight out the side, which may be good for your graphics card but not good for your CPU.
I don't think its too much of a concern, if your graphics card has an aftermarket cooler then it'll run cool regardless of whether the side fan is intake or exhaust.
Anyway thats just my thoughts. Nice card btw