Noise is never a good thing in a hydraulic system, this is especially true if the noise changes between when the pump is on or off stroke.
Most likely the pump is experiencing some degree of cavitation, which is causing the noise. The life of the pump, and the operation of the system are negatively affected by this situation. One cause of cavitation is the pump is not able to get all the oil it needs on the suction side. The other is the oil flowing into the pump has air bubble entrapped in the fluid. The first thing to check is the oil level in the reservoir at it low point. When all the cylinders are extended is the inlet of the pump well covered? Normally in a well designed system, the oil level must always be visible in the site gauge. The second thing to check is the inlet suction filter. Sometimes these filters are accessible outside the tank, but most often they are a screen submerged in the reservoir. Even if it means draining all the fluids, this inlet filter needs to be checked and cleaned. The third step is all the hoses and connections on the suction side need to be checked or tightened. After these three steps, if the oil is milky looking in the reservoir, but clears when the oil is allowed to sit, air is entering the system from somewhere. Check all hoses, and tighten all fittings and connections, until the source of the air entering the oil is found and eliminated