Are you using Goulds' centrifugal pump? This sounds like there may be a suction vortex on the intake of the pump. If there isn't enough water covering the intake pipe in the holding tank, the water may start to swirl when the pump comes on and the vortex grows all the way down to the intake and that's how air can get into the system. It's very much not good for the pump, too - can lead to broken impellers, noise, vibration and just generally increased wear. You can address the suction vortex by either decreasing the water flow or raising the level of water in the tank. If the amount of water the pump provides is just enough for your use, lowering the water flow (through using a smaller pump for example) is not a very good option, increasing the tank water level seems an easier alternative.
There should be a float switch in the holding tank, adjust it so that the water level in the tank goes up. Hard to tell how much to raise it although formulas do exist (see picture below, courtesy of Xylem/Goulds). You should also be able to find a good position by just trial and error. The idea is to find a position where the pump no longer makes any rumbling noises or knocks which result from the air in water going through the pump.