Except Staten Island had the second most cases per capita. Lots of the obvious NYC theories have holes where you look at places affected.

People who live or work on Staten Island used mta services, including subways, heavily.

Maybe ferries cause the same kinds of problems as subways do.

Yes Public transport is probably the best use case for contact tracing. A combination of location history and fare card data will work for buses. For trains it's a bit trickier since you want to resolve that you're in the same car, and Bluetooth would work well in this case.