Here are the following off off Broadway theaters that I know of or have attended. All have less then 100 seats.
In Brooklyn: JACK, The Bushwick Starr, the Brick
In Manhattan Abrons Arts Center has three theater venues and two of them are less then 100 seats.
the Ohio Space and the Wild Project are two more.
these are just a few that come to mind immediately. Many theater projects that are considered off off are now put on in Pop Up Spaces, sometimes in the
apartments of the participants.
Oh yes, Queens---The Secret Theater and one that I am blocking now.
I hope this helps.