[woodruffw]

The MTA is not a state agency at all; it’s a public corporation owned fully by the state. The governor has the ability to appoint some members of the MTA board, but can only appoint a minority of members.

I’m not aware of any special powers still in effect; it would be good to have a link for that.

[PLenz]

A distinction without a difference. Corporations and authorities owned but the state are state agencies, the confusion on this point is a feature by their investor, Robert Moses, to give himself maximum power and minimum oversight. As to state control over the city- it's in Title IX of the NYS Constitution

[woodruffw]

It’s a distinction with a significant difference: the MTA’s board has a unique fiduciary duty to the Authority that a state agency’s leadership does not have. As noted above, it is also not a “purely” state-level authority, unlike the type Moses was fond of creating (which is among the reasons he opposed merging NYCT into it).

Title IX of the NYS Constitution describes the general terms of home rule, including the rules that govern all counties, towns, and cities within the state. I can’t find an explicit reference anywhere to NYC or its countries anywhere within that title, so I don’t know which section you think implies “special powers.”

[PLenz]

Title IX includes a "state interest" clause which the courts have interpreted to mean that state can stick it's nose into any local issue it wants to.

[woodruffw]

Okay. That isn't a "special powers for NYC" clause, that's a generic "home rule is not absolute" clause. Nobody has said or implied otherwise; the operative question was whether NYC is any different from other municipalities in terms of limits on the scope of its home rule.

(If anything, NYC is afforded an unusual degree of home rule relative to other municipalities in NY, as evidenced by the fact that it's really 5 counties in a trenchcoat.)