My God, this is almost as bad as religion.
It depends on heatsink design, & the environment in which it is installed. Some coolers are specifically designed for "blowing" rather than "sucking," such as the Agilent ArctiCooler. Some are specifically designed for "sucking," such as the copper HedgeHog & the venerable Alphas PXX6035 line. HS's that have sucking in mind may have a shroud around them to ensure that air flows through as much of the heatsink as possible.
Bottom line? TRY IT! Most modern motherboards have temperature monitoring functions, at LEAST in the form of a temperature probe. You probably won't see more than a couple degree difference anyway, it's not like one way is going to hose your CPU.
Viper GTS