The longest IND exit that isn't there any more is the mezzanine level passage which once connected the 34th Street and 42nd Street (6th Ave) stations. It had street entrances at 38th Street, which is the reason it was built - to replace the 38 St stop of the 6th Avenue el. Entering at 38th, you could walk two blocks north or 3 blocks south underground to enter the system.
This passage was closed in the late 70's or early 80's, as I recall. It had become a home to many homeless, but the catalyst which led to its closing was a murder in the tunnel. I don't recall whether one of the "residents" was involved, either as victiim or perp, but that was the final straw - it was closed soon after.
The stairways at 38th are gone and invisible from street level. Walls were built to seal off the passage. There are doors in the center of the mezzanine ends at the north end of 34th St station (north side 35th St) and south end of 42 St station (south side 40th St). They are are sometimes left open for employee access, and from occasional glimpses, it appears the TA has built a huge storage/work area in the passage. Image what you can store in a space 5 blocks long, the full width of an avenue.
While not strictly an IND passage, there was also a pedestrian tunnel under 33rd St connecting the 34th St-6th Av station to the IRT 33rd Street-Penn Station stop. Closed about the same time as the long mezzanine, the east end of this tunnel can be seen as a padlocked black metal door just, south of the new elevator between 34th and 33rd. The west end has been hidden behind new tiling as part of the recent renovations on the IRT end. This tunnel also had direct access to Gimbels (now Manhattan Mall), the Pennsylvania Hotel and, of course, Penn Station.
Before the realignment of the fare controls at Herald Square, it was possible to walk outside of fare control from the north to south end of that station. Thus, once upon a time, you could go downstairs at 40th & 6th, and emerge at the SW corner of Penn Station at 31st & 8th, 9 blocks south and 2 blocks west. This was undoubtedly the longest free underground walk in New York!