According to that wonderful New Yorker article of Trillin's, this particular pumpernickel bagel also had onion in it, unusual all by itself, along with the lack of boiling.

You may do well seeking out a Jewish-stype pumpernickel bread recipe and adpating it to bagel shape, and flavoring it with onion, as a review of the article in question implies the bagels actually came from a bread bakery as opposed to a bagel bakery (the article has delightful details of that difference, too).

The closest I come these days to the old-fashioned Jewish pumpernickel of my youth is made by Cohen's in Ellenville, NY, and the loaf contains raisins. I'd love a recipe that duplicated that bread, but I bet with some onion and no raisins, it'd work.

Boron

While your hunting down the perfect recipe, try ESSA bagels in NY on 50th and 3rd (and one on the lower east side too).  Best bagels ever, including pumpernickel with raisins, but best is without raisins and with sesame, perfect match for pumpernickel.  Large, boiled, and chewey on outside, soft inside.  Best bagel ever made, and better than the touted H&H...  The gold standard. 

Most bagel stores (and bakeries) use caramel coloring to get the dark "pumpernickel" color we are so used to seeing.  The truth is that even 100% rye/pumpernickel is lighter in color, more like whole wheat if no darkening additives areused.   ESSA surely does too but I don't hold it against them.  In fact most pumpernickel bagels have more white flour than whole grain, but hard to tell given the coloring.

Since I couldn't find what I was looking (or even know what I was looking for), I made my own version of pumpernickel bagels. I used the BBA recipe using pumpernickel flour for the sponge portion of the recipe and high gluten for the final dough. In half the batch I knead in raisins and the other half dehydrated onions and topped them with onion.

They came out very tasty.