Same as usual I guess.
If after silence, and the 200mm fans can be ran low enough (enough airflow performance). They will be taken as the choice.
If after performance (just air being blown at full speeds), then reading a rough guide on the fans (I just took a quick gander at Noctua as they have 140mm and 200mm fans) and it looks like the 140mm will provide more airflow in total. So the 140mm will be the choice if after that.
If after a combination of performance and silence, then it really depends on how high your tolerance to noise produced is. Typically the larger fans will run slower rpms at max performance and in theory should provide less noise. But this really does depend on your case you house them as well. Since some more flimsy panels will echo and vibrate from the airflow and cause annoyance for those who can hear it. Badly structured internals will also yield aggrevating sounds if you increase airflow through/onto them. So I would really take this as a matter of goals you have; Both fan ideas appear just as valid as the other, but would depend entirely on your personal goal for them.
Silence (what your ears can/will tolerate), or Airflow at full (when you need to cool the system no matter what).
In a pinch, your PSU may also be a determining factor, as it might not have enough power to run everything (as I recently found out to my dismay after adding more fans to my rig and the PSU wasn't having it when I heavy loaded the system). In which case the 200mm fan may be more desired for the lower power requirement.
