I have a 3-D array where the first column is month, the second column is city, and the third column is a vector of temperature of the city in that month.
So the array has size [N 3] for some value of N? That's not a 3-dimensional array. That's a matrix with three columns.
Then I now want to create a 3-D array where the first column is month, the second column is city, and the third columnis the n-th highest temperature of the month of the city.
I'm going to assume you mean that you want another matrix with three columns. As you've described it, you should use the groupsummary function. You can use the "Multiple Grouping Variables" or "Multiple Grouping Vectors for Vector Input" examples on that documentation page as a model.
