This paper presents a robust and efficient boundary element method (BEM) for predicting underwater electromagnetic (EM) noise generated by permanent magnet synchronous motors (PMSMs) in rim-driven thrusters (RDTs). Compared to the Finite Element Method (FEM), the BEM has distinct advantages in handling exterior acoustic problems, such as easier implementation of Sommerfeld radiation condition, reduced mesh requirements, and lower discretization errors. However, when applied to the problem of EM noise in RDTs, the traditional BEM has two main drawbacks. First, the conventional BEM tends to produce fictitious modes at high frequencies. Second, due to the dense and frequency-dependent nature of the BEM matrices, the method suffers from low efficiency in large-scale frequency sweep calculations. To overcome the aforementioned drawbacks, the proposed method incorporates the Burton-Miller formulation to suppress fictitious modes and a Taylor expansion method for efficient frequency sweep calculations. Numerical experiments on a 96-slots, 16-poles PMSM validate the accuracy and efficiency of the proposed method. Additionally, this paper investigates fluid loading effects on the structural vibrations, providing insights for the design of vibration and noise reduction strategies in underwater motors.