Before talking about entropy, we need to discuss what possible states an atom can be in. I will start by the most general case that consists in considering a single-atom gas in a 3D box. In that case, the microstate of the atom is described by:
The definite linear momentum states $| \textbf{k} \rangle$ of the atom (that are eigenvectors of the hamiltonian)
Its internal state characterised by given a list of quantum numbers like $|n, \ell, m_{\ell}, s, m_s \rangle$
If there is not enough energy in the system to excite the atom from its ground state, then only its momentum state matters to compute its statistical properties, if furthermore the de Broglie wave length of the atom is small compared to the box size (or confinement size for some cooling techniques), then the atom states can be accounted for by the position of the center of mass of the atom in phase space $(\textbf{r}, \textbf{p})$.
When performing laser cooling of a gas, a big part has to do, initially at least, with a drop in the dispersion of velocity; by definition of cooling. That is because gas cooling (in the context of cold atoms) is firstly performed by taking care of the (classical) momentum dispersion by applying a force in the direction opposite to that of the gas jet/ atomic beam. That is the principle of many laser cooling or fountain-like devices at least.
Overall, if the gas density is considered unchanged during the cooling and the temperature changes from $T_h$ to $T_c$, then one can expect an entropy change per atom that is well approximated by:
\begin{equation}
\Delta S = -\frac{k_B}{2}\ln \frac{T_h}{T_c}
\end{equation}upon being cooled down from $T_h$ to $T_c$.
Note that I have put $k_B/2$ instead of $3k_B/2$, that is because in most of the preparations I know, molecular effusion is used to generate the initial beam of atoms. Such a beam has generally a low statistical dispersion in the directions perpendicular to the jet axis (and thus somehow lower temperatures for those degrees of freedom) and moreover, these degrees of freedom are untouched by either standard laser cooling or gravitational fountains.
Of course once the stage of trapping of the gas occurs by combining, say, lasers and magnetic fields, then one would have to add again this factor 3 but also to eventually take into account the quantum effects: discreteness of the momentum spectrum and quantum fermonic or bosonic statistics at sufficiently low temperatures.
Remark 1: While the beam is being cooled in the first stage, one could also add that there is a slight increase of entropy due to the dispersion of the gas in the direction perpendicular to the beam's axis. I haven't accounted for it in the formula I have given.