It looks like Long Tall Sally had (has?) a pop up store at 25 Greene Street. Probably not open now, but it wouldn't hurt to check.
New York & Company stocks tall pants in store, but you really have to watch the quality. I've got a couple great pairs of pants there over the years, but I've tried on, and rejected, dozens more. The Limited stocks tall sizes in my Midwest state, and Old Navy stocks some jeans in tall sizes.
Otherwise, I sometimes have success in stores such as Banana Republic or J Crew if I check the clearance rack. If someone returns a tall size in store, it goes on the clearance rack, and you can occasionally score something really good for a fraction of the original price. (operative word is "occasionally.").
Finally, Nordstrom, Nordstrom Rack, Macy's, and other department stores always have a few pants and jeans with long inseams mixed in with the rest; you just have to be persistent to find them. Now that I think about it, Macy's I.N.C. brand stocks tall pants in store.
Good luck, and let us know if you find something good.