Obviously you'd have to use passing yards to find out who leads the NFL in passing yards. But the NFL doesn't use yards to rank its passing leaders, it uses passer rating. In fact, it's the only reason passer rating even exists.
Timeline of Methods Used by the NFL to Determine Passing Leaders
Since the NFL first started keeping official statistics in 1932, the following are the different ways in which the passing champions were determined.
1932-1937
Total yards passing
1938-1940
Percentage of completions
1941-1948
Inverse ranking system of the following categories: completions, percentage of completions, total yards, total TD passes, number of interceptions, and percentage of interceptions.
1949
The same formula used from 1941-48 except the number of interceptions was dropped from the equation.
1950-1959
Average yards gained per pass with a minimum of 100 attempts needed to qualify.
1960-1961
Inverse ranking system based on six categories: total completions, total yards, total TD passes, percentage of completions, percentage of interceptions, average gain per attempt with the principle established of at least 10 attempts per game to qualify.
1962-1971
Inverse ranking system based on four categories: Percentage of completions, total touchdown passes, percentage of interceptions, average gain per attempt.
1972
Same system used from 1962 to 1971 except that the percentage of touchdown passes was substituted for total touchdown passes.
1973-present
Passer rating.
https://www.profootballhof.com/news/nfl-s-passer-rating/
http://www.nfl.com/history/randf/records/indiv/passing