Harvard has the most clerkships because they have the largest cohort by far, at around 500. Yale is widely considered to be the most prestigious law school in the US. Historically, they have had the lowest acceptance rates and highest percentage of graduates heading into academia. Also low class sizes means its spending per student is through the roof. Many Harvard professors at Harvard law school are Yale alumni.

It is only outside the states that people have the misconception of Harvard > Yale law, because Harvard is the more internationally renown university. Most applicants would turn down Harvard/Stanford for Yale.