Recently, several methods have been proposed for estimating the mutual information from sample data using deep neural networks and without the knowledge of closed-form distribution of the data. This class of estimators is referred to as neural mutual information estimators (NMIE). In this paper, we investigate the performance of different NMIE proposed in the literature when applied to the capacity estimation problem. In particular, we study the performance of mutual information neural estimator (MINE), smoothed mutual information lower-bound estimator (SMILE), and directed information neural estimator (DINE). For the NMIE above, capacity estimation relies on two deep neural networks (DNN): (i) one DNN generates samples from a distribution that is learned, and (ii) a DNN to estimate the MI between the channel input and the channel output. We benchmark these NMIE in three scenarios: (i) AWGN channel capacity estimation and (ii) channels with unknown capacity and continuous inputs i.e., optical intensity and peak-power constrained AWGN channel (iii) channels with unknown capacity and a discrete number of mass points i.e., Poisson channel. Additionally, we also (iv) consider the extension to the MAC capacity problem by considering the AWGN and optical MAC models.