For most passengers, the two figures are the same. The difference is for passengers on a one-stop route. These passengers count as one enplanement, but two onboards.
So someone flying WN IAD-MDW-PHX on the same plane actually only enplanes once, but is counted onboard both legs.
This distinction used to be more meaningful in the days when flights had many stops, but with the advent of nonstop flights and large hubs, the numbers are generally within a percentage point of each other.