Lincoln Center Theater has had a table in the past, and has things from shows that closed earlier in the season/year (I bought a signed Women on the Verge windowcard at the Flea Market held the September after the show closed), and they MIGHT have leftover merchandise from several seasons, but there's obviously no guarantee.
As for shows that are no longer running, it depends. Sometimes tables from shows that are currently in the theater where the closed show was have some merchandise. There are usually several tables with just a mishmosh of things (often run by merchandise companies), and you can always find some nice surprise. Depending on what you're looking for, you should be prepared to spend a lot of time digging around tables.
When I see the phrase "the ____ estate", I imagine a vast mansion in the country full of monocled men and high-collared women receiving letters about productions across the country and doing spit-takes at whatever they contain.
-Kad