Kinda depends on the rest of your cooling setup. I prefer using intake for water (think car radiator), but you must have good exhaust using this setup to make sure the additional heat being put on other components is dissipated quickly.
You really need to make sure you maintain positive pressure using it as intake - i.e. more exhaust than intake. All that said, using the rad as exhaust at the rear also works as it does slightly lessen temps on other components at the loss of a small margin of cooling effectiveness for the rad. Again, make sure you have positive air pressure in the case.
Bottom line - for a cooler that size, it probably won't make much of a difference as long as you maintain more intake than exhaust.
Mark