In this paper, we develop a tractable analytical framework for a three-dimensional (3D) indoor terahertz (THz) communication system to theoretically assess the impact of the pointing error on its coverage performance. Specifically, we model the locations of access points (APs) using a Poisson point process, human blockages as random cylinder processes, and wall blockages through a Boolean straight line process. A pointing error refers to beamforming gain and direction mismatch between the transmitter and receiver. We characterize it based on the inaccuracy of location estimate. We then analyze the impact of this pointing error on the received signal power and derive a tractable expression for the coverage probability, incorporating the multi-cluster fluctuating two-ray distribution to accurately model small-scale fading in THz communications. Aided by simulation results, we corroborate our analysis and demonstrate that the pointing error has a pronounced impact on the coverage probability. Specifically, we find that merely increasing the antenna array size is insufficient to improve the coverage probability and mitigate the detrimental impact of the pointing error, highlighting the necessity of advanced estimation techniques in THz communication systems.