The $q$-analog of Kostant's weight multiplicity formula is an alternating sum over a finite group, known as the Weyl group, whose terms involve the $q$-analog of Kostant's partition function. This formula, when evaluated at $q=1$, gives the multiplicity of a weight in a highest weight representation of a simple Lie algebra. In this paper, we consider the Lie algebra $\mathfrak{sl}_4(\mathbb{C})$ and give closed formulas for the $q$-analog of Kostant's weight multiplicity. This formula depends on the following two sets of results. First, we present closed formulas for the $q$-analog of Kostant's partition function by counting restricted colored integer partitions. These formulas, when evaluated at $q=1$, recover results of De Loera and Sturmfels. Second, we describe and enumerate the Weyl alternation sets, which consist of the elements of the Weyl group that contribute nontrivially to Kostant's weight multiplicity formula. From this, we introduce Weyl alternation diagrams on the root lattice of $\mathfrak{sl}_4(\mathbb{C})$, which are associated to the Weyl alternation sets. This work answers a question posed in 2019 by Harris, Loving, Ramirez, Rennie, Rojas Kirby, Torres Davila, and Ulysse.