It is difficult to answer without knowing what your current heat sink is. However, in general heat dissipation through the cooler would be the better upgrade if you're using stock cooling. Heat transfer from the cooler to the air is more important (very generally speaking) than air flow itself. However, both are important variables, so if your cooler is aftermarket you would then want to increase airflow through the case in some way as the next improvement.
Again, very generally speaking.