Yes, I put more faith in FiveThirtyEight. I'm guessing you don't read the NYT or follow American politics, so I'll fill you in on FiveThirtyEight's bona fides. The founder, Nate Silver, helped pioneer big data analytics in sports and politics. In 2012, he and his group correctly predicted the outcomes of all 50 states in the Presidential election, and he authored a NYT best seller that went on to be named the number 1 non-fiction book of 2012 by Amazon.com. That's not to say that there was as much thought put into this particular poll, but this type of polling is one of their areas of expertise.
Rotten Tomatoes is useful, but not in a scientifically rigorous way. Their aggregate system is a dubious way to measure something like a film's "quality". In the FiveThirtyEight poll, people were asked specifically to pick the best movie out of the six, and only the responses from people who had seen all six movies were considered. The RT "study", on the other hand, was not a head-to-head comparison. The reviewers of one movie may not have even seen the others, or may not have submitted a review for the others. To further muddy the water, the RT "study" cherry-picked original release reviews. This is a questionable methodology because it ignores contextual biases. For example, Jedi may have been perceived as a disappointment because it directly followed A New Hope and Empire. Similarly, Eps I and II set the bar pretty low for Sith. On the other hand, one could argue that the prequels were such an unfamiliar departure from the OT that it artificially deflated their initial reception. These contextual biases make an objective comparison difficult, particularly when comparing reviews from two narrow and distinct time frames. Keep in mind that these reviews, assigned a number score, were written within the context of their respective contemporary summer blockbusters. Furthermore--even without consideration to those contextual biases--there are many films currently celebrated as classics that were dismissed by critics upon their debut, only to be rediscovered and re-appraised years later. Critics change their minds, films grow or diminish in stature, and this project ignores all of that to arrive at its conclusion.
No study, poll, or person is completely free from biases, which is what allows this debate to continue on ad naseum. However, when trying to gauge consensus opinion among fans, the most appropriate type of poll is one which ranks the films relative to one another (i.e. head to head).
I will say that this debate has been somewhat illuminating to me. I had no idea that there were people in the world who would argue for any of the PT over any of the OT. Even the attached IMDB results surprise me.