The biggest, densest city in the country being below-median among other major cities for that stat still seems pretty good to me! Particularly since 1. NY is dragged above the national average on the cumulative stat by what are arguably “less severe” violent crimes (i.e. not murder, rape) and 2. Almost every city ranked better on that stat is very small comparatively, only two have >1M people. Every city that you could really consider a real peer of NY (LA, SF, Chicago, Miami, etc.) does worse.
Also, when ranked by that total the “best 4” aren’t really the best 4. They don’t report rape numbers, so they don’t get a total. And their numbers are all worse than NY on the other categories (murder, robbery, assault).