We pursue our study of integrable weak noise theories of directed polymer and interacting particle stochastic models in the 1D KPZ universality class. Here we focus on the $q$-TASEP in either continuous or discrete time. Each particle on $\mathbb{Z}$ jumps independently by $+1$ with a rate (or probability) depending on the gap to the next particle on its right. We consider initial conditions (either step or random) which are empty of particles on $\mathbb{Z}^+$, and focus on the dynamics of the $N$ rightmost particles. In the limit $q \to 1$ and at large time (and large gaps) we identify a new intermediate "mesoscopic" (i.e. finite $N$) regime which corresponds to weak noise. In that regime Poisson noise remains important. We obtain the large deviations of the position of a given particle by two methods. The first derives asymptotics of $q$-TASEP Fredholm determinant formula. The second maps the weak noise limit to a system of semi-discrete or fully discrete, non linear differential equations. These are obtained as saddle point classical equations of a dynamical field theory, and their solutions represent the optimal configurations in the large deviation regime. We show the classical integrability of these two systems, and exhibit their explicit Lax pair. In the case of the continuous time $q$-TASEP it provides the first instance of classical integrability arising in a stochastic system, with signatures of the Poisson noise persisting in the weak noise limit. For this model, we solve the scattering problem associated to its Lax pair and fully characterize the large deviations associated to the weak noise theory. Finally, we supplement this work with an Appendix on the first cumulant method to obtain the large deviations of several lattice polymer models (Strict Weak, Log Gamma, Beta).