The answer (if I actually got it right), for anyone still wondering:
Let $\mathbf{e}_1,\mathbf{e}_2,\ldots,\mathbf{e}_k$ be a basis of $U$, $\mathbf{f}_1,\ldots,\mathbf{f}_l$ be a basis of $V$ and $T:U\rightarrow V$ be a linear map.
Then
$$T(\mathbf{e}_1) = \alpha_{11}\mathbf{f}_1 + \alpha_{12}\mathbf{f}_2 + \cdots + \alpha_{1l}\mathbf{f}_{l}$$
$$T(\mathbf{e}_2) = \alpha_{21}\mathbf{f}_1 + \alpha_{22}\mathbf{f}_2 + \cdots + \alpha_{2l}\mathbf{f}_l$$
$$\vdots $$
$$
T(\mathbf{e}_k) = \alpha_{k1}\mathbf{f}_1 + \alpha_{k2}\mathbf{f}_2 + \cdots + \alpha_{kl}\mathbf{f}_l$$
defines $T$. The number of different linear transformations is then just the number of different combinations of $\alpha_{ij}$'s. There are a finite number of combinations as there are only $q$ choices for each one.
I found two similar methods, each with a slightly different focus, that lead to the answer:
More algebraic
As there are $q$ different choices for each $\alpha_{ij}$ and they are chosen independently, so on each row there are $q^l$ different choices. Now over $k$ independently chosen rows we have
$$\underbrace{q^l \cdot q^l \cdot \cdots \cdot q^l}_{k\text{ times}}=(q^l)^k=q^{kl}$$
different choices
More combinatorial
we may write the linear transformation as a matrix of the coefficients ($\alpha_{ij}$'s) in the following way
$$
\pmatrix{
\alpha_{11} & \cdots & \alpha_{1l}\\
\\
\vdots & \ddots & \vdots\\
\\
\alpha_{k1} & \cdots & \alpha_{kl}
}
$$
You can now look at the number of ways of choosing combinations of non-zero $\alpha_{ij}$'s, which is every possible matrix and therefore every possible linear transformation (note that choosing no $\alpha_{ij}$ non-zero gives us the zero matrix).
There are
$\binom{kl}{0} \cdot (q-1)^0 = 1$ ways of choosing no non-zero coefficients. We are choosing zero of the $k \times l$ coefficients.
$\binom{kl}{1} \cdot (q-1)^1 = (q-1)$ ways of choosing one $\alpha_{ij}$ non-zero. 1 of the $k\times l$ coefficients and $q-1$ different choices for it
$\binom{kl}{2} \cdot (q-1)^2$ ways of choosing two $\alpha_{ij}$ non-zero. There are $q-1$ non-zero choices for each of the 2 coefficients, so $(q-1)^2$ different combinations
In general there are $\binom{kl}{i} \cdot (q-1)^i$ ways of choosing $i\ \alpha_{ij}$ non-zero. The total number of linear transformations is the number of different matrices, which is the sum of all the numbers above:
$$\sum_{i=0}^{kl} \binom{kl}{i} \cdot (q-1)^i = \sum_{i=0}^{kl} \binom{kl}{i} \cdot (q-1)^i \cdot 1^{kl-i}= (q-1+1)^{kl}=q^{kl}$$