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 pH is a logarithmic scale, where each whole number change in pH represents a tenfold change in hydrogen ion concentration. Therefore, a difference of 3 units in pH (from 3.0 to 6.0) corresponds to a 10^3 or 1,000 times difference in hydrogen ion concentration.