The correct statement is:
The substance with the lower pH has 1,000 times as many hydrogen ions per volume of water.
This is because the pH scale is logarithmic: each whole number change on the scale represents a tenfold change in hydrogen ion concentration. A pH of 3.0 is three units lower than a pH of 6.0, which means the concentration of hydrogen ions is \(10^3\) or 1,000 times greater in the substance with pH 3.0 compared to the substance with pH 6.0.