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, which means that each whole number change on the scale corresponds to a tenfold change in hydrogen ion concentration. Therefore, a pH of 3.0 is 1,000 times more acidic (has 1,000 times more hydrogen ions) than a pH of 6.0.