1. St. Louis, MO -38%
2. Hoboken, NJ -31%
3. Scranton, PA -29%
4. St. Joseph, MO -26%
5. Wheeling, WV -26%
6. Buffalo, NY -23%
7. Troy, NY -22%
8. Wilkes-Barre, PA -21%
9. Fall River, MA -13%
10. Holyoke, MA -12%
11. Harrisburg, PA -5%
12. Wilmington, DE -4%
13. Pittsburgh, PA -3%
14. Albany, NY -0%
15. Providence, RI -0%
16. Covington, KY +0%
17. Cincinnati, OH +2%
18. Reading, PA +3%
19. Utica, NY +3%
20. Camden, NJ +4%
Pittsburgh would be in second place, with about a 35% loss, if you include the population of Allegheny, a city which it absorbed a few years later. Allegheny was the 27th biggest city in its own right in 1900.
The big surprise to me was St. Joseph, which was the 34th largest city in the country in 1900. That didn't last long--it lost about a quarter of its population, and has stayed about the same ever since. Another surprise was that Providence was the 20th biggest city in the country in 1900. Its estimated population in 2009 was within 100 of its population in 1900.