beating out NYC, for which it has 1/10 NYC's ridership.

You can't compare a relatively new / modern system with a over 100 year old subway system in NYC. If NYC did not build a subway system 100 years ago, but would do so now it would probably cost much less too. Let the elevated railway age a little bit more, and tremendous costs will occur, while the entire route is out of service.

The public transport system in Berlin (mix of street cars, busses, ferries, and light rail on separate rails and subway) is profitable too. The city owns the public institution as it does with many other companies that are profitable like the municipal power company, they all run well and are profitable.

I don't think that one system is better than another. It's how you run a company or public institution. If it's public it's a political question whether you want the company (public transit) be profitable or not.

Legacy costs of previous City employees, now spending their pensions i

That was stopped in Berlin too. Most employees of public institutions were state of municipal officials with high pensions and state benefits, today they are all public service employees, treated like any other free market employee. Maybe that's why public transit isn't profitable in the US.