The same article also qualifies that information with this statement:
Salaries are different between the classes in the minors, and it is here that the complexities arise. The information provided shows average salary, but the mean of the these brackets can be skewed by a small number of players earning higher pay, unlike median salary which would have largely normalized the data.
The point is there are two kinds of players at Triple-A – guys who have been there and guys who haven’t. For example, if one veteran (say with MLB experience) makes $20K per month and four others make $2.5K each (still above minimum), that averages $6K per player. One is paid well and four are not.
But even if $10K average is accurate, that is $50K per season, not $90K. And Double-A would be $30K per season. Players are paid for April thru August.
In the Cardinals system, about 80% of the Minor Leaguers are below Triple-A and Double-A.