Their materials carefully imply that they aren't, but in my experience all theaters are pretty much covered. Even the small artsy theater ran by a local non-profit.
In my experience, most of the theaters in NYC are covered (including all the AMCs) but there are a small few arthouse theaters that aren't covered. That said, there are plenty of arthouse theaters in NYC that _are_ covered, so it's not a problem at all for me.
A bigger issue (for some people) is that it doesn't cover 3D films and other such fancy versions of films that also have regular versions. I personally don't care (I don't like the 3D ones) but I imagine that could be undesirable. Though, technically, there's nothing to stop you from using moviepass to see those kinds of things, but it's against their rules, so if they catch you they could cancel your subscription. I'm not sure how aggressively they check up on those things though.