You shouldn't flag based solely on the presence of key words, like "best". Don't let those short-circuit your brain and prevent you from analyzing the question on its own merits.
The "primarily opinion-based" flag/closure reason states:
Many good questions generate some degree of opinion based on expert experience, but answers to this question will tend to be almost entirely based on opinions, rather than facts, references, or specific expertise.
Do you think that applies here? It is not clear me to me that it does. I suspect the other users who looked at the question after you flagged it were similarly unsure. (Note that "disputed" means it was not a moderator who evaluated your flag. It was 3–5 other experienced users who saw it in the review queue. They disagreed that the question needed to be closed.)
I agree that "better" is not the—err… best—choice of wording for this question. It would be "better" if the asker would edit the question with a more objective criterion on which to base the decision. But while that would improve the question and make it definitively not opinion-based, I don't even think the question as it currently stands is "primarily" opinion-based. It seems perfectly reasonable to expect that answers will be based on "facts, references, [and] specific expertise", rather than entirely on opinions. Imagine that he had presented the two options, and then asked what is the difference between the two. Assuming that the differences are not so numerous as to make the question "too broad", this would be a perfectly valid question, and not one whose answers are primarily based on opinions.