Totally subjective and nearly impossible to say with any certainty.
My personal list of the greatest race horses ever:
Greatest Colt: Man O' War
His lifetime record included 21 starts with 20 wins and a one place finish. He retired as the leading money winner in North America at the time. He set 8 records, 3 world records, 2 North American records, and 3 track records all by more than just a fraction.
Man O' War also carried as much as 138 pounds, conceding as much as 30 pounds to his rivals and still beat them by large margins. Another factor was the level of vetenary medicine during his day and the modern state of the art medicine available to contemporary horses.
Greatest Filly/Mare: Tie - Personal Ensign or Ruffian.
Greatest rivalry: Seabiscuit and War Admiral.
Honorable Mention: Northern Dancer and Secretariet, Seattle Slew. There are so many others who could easliy make this list.
wil..