Investigating the coil–magnet structure plays a significant role in the design process of the electromagnetic energy harvester due to the effect on the harvester’s performance. In this paper, the performance of four different electromagnetic vibration energy harvesters with cylindrical shapes constrained in the same volume were under investigation. The utilized structures are (i) two opposite polarized magnets spaced by a mild steel; (ii) a Halbach array with three magnets and one coil; (iii) a Halbach array with five magnets and one coil; and (iv) a Halbach array with five magnets and three coils. We utilized a completely automatic optimization procedure with the help of an optimization algorithm implemented in Python, supported by simulations in ANSYS Maxwell and MATLAB Simulink to obtain the maximum output power for each configuration. The simulation results show that the Halbach array with three magnets and one coil is the best for configurations with the Halbach array. Additionally, among all configurations, the harvester with two opposing magnets provides the highest output power and volume power density, while the Halbach array with three magnets and one coil provides the highest mass power density. The paper also demonstrates limitations of using the electromagnetic coupling coefficient as a metric for harvester optimization, if the ultimate goal is maximization of output power.