There are many schools of thought surrounding the subject of building a 331 or a 347, most of those schools of thought are conflicting and I'm just talking about the professionals that build and tune both on a regular basis...that doesn't count the average "gearhead" that has an opinion based very little on their own experience and mostly on the hearsay and rumors recounted by other gearheads.
Here's the truth about the controversy: a 347 has two things working against it in comparison to a 331: A lower rod to stroke ratio (which means more potential cylinder wear) and increased piston speed and subsequent friction.
In a situation where longevity at high RPM is paramount, a 331 will out perform a 347 and quite frankly, chances are the extra 10-15 horses or torque you may gain out of the combination isn't going to make that much difference.
In the case of driving on the street or racing where max longevity of the motor in extreme wear conditions isn't paramount, the 347 is going to work better, provided it is built correctly.
The reality is this: Getting the very last ounce of performance out of the different combos isn't going to be within the means of the average gearhead. It's been my experience that most gearheads can't even make their combos run well, much less extract every bit of performance from them.
It is my experience that if you go with a good build, you will benefit from a 347 as it will make more power even if the combo isn't optimum. And, the larger displacement can make up for the lack of optimized combination which will become more and more necessary the smaller the motor is.
On the other side of the coin: Putting a small blower on a 302 is going to make the same amount of power as a mildly built N/A stroker and will be cheaper to do, especially since there are blower kits on the market that come "tuned" to work with your stock components.