Generally I think it is actually pretty much safe unless it has rained heavily recently. The last time I looked at the data, much of the harbor and Hudson have bacteria counts that are consistently within the safe-for-bathing parameters. The East River is the most polluted, however it also has strong and changing currents that make it less interesting for swimming.
Ultimately I think there’s just kind of a general inertia against it—a public perception that the water is gross (as it certainly was for generations), lack of facilities to easily enter the water, and a city government that’s not especially interested in promoting it, probably for liability reasons primarily.
Personally I’d love to see the Central Park reservoir made into a swimming place. As I understand it, it’s never actually used as a reservoir anymore and would be perfect for swimming if they built an entry point. Instead they arrest people who get in.