The statue shows Roosevelt on a horse, flanked by a Native American and African American. You can't ignore that it is some type of representation of Roosevelt leading the others in some way. Exactly what it means is open to interpretation, and even can change in time. So honor Roosevelt appropriately with a statue of just him. Once you have representations of multiple people in a statue or other memorial, how you present them can start to imply a narrative of hierarchy, and I don't think that is what Roosevelt was about.
For comparison, and also in New York City, the American Merchant Mariners' Memorial in the Hudson river is a powerful memorial with no hierarchy, just a group of sailors struggling in the ocean. It's an incredible work, and to see it in person, with an unknown sailor reaching for life really captures the sacrifice of these sailors. Similarly, the statue of George Washington at Federal Hall in NYC, a few blocks away, shows an image of Washington being sworn in to office, but keeps the focus on Washington himself as an idealized character.
So I'm fine with relocating the current statue and installing a better one of Roosevelt. These types of art are meant to be idealizations, so we should idealize our best aspirations. America is great because it offers opportunity and self determination over the hierarchy and artificial barriers imposed in other places. I believe some of our best attributes is our culture of individual freedom and self determination, and I think we should remind ourselves of that.