This branch just opened. I know it's a chain, but I called and was told the bagel dough is mixed at the store from scratch every day. I even verified that they don't use a pre-made mix and "just add water". Rather they mix ingredients from separate containers together and form their dough. When you walk in, you can actually watch them mixing the dough, shaping the bagels, boiling, and then baking.
We sampled plain bagels and "the last bagel that came out of the oven", which was a sesame bagel. The plain bagel had a nice crisp exterior and a chewy interior. The interior was denser and chewier than I expect from "NY-style bagels", but I've been told that this is how Brooklyn-style bagels are supposed to be. The interior had a distinct malt-like taste, but not as strong as what you might find in a soft pretzel. I am no bagel expert, but it was enough to convince us to return and see if the experience holds up with repeat visits.
The exterior of the sesame bagel wasn't as crispy as the plain bagel, and one half of the sesame bagel's interior wasn't as airy as the other half. Likely this means whoever was hand shaping the bagels messed up a little, but at least it was handmade.
I was told the muffin and cookie batters are also formulated at the store. (As opposed to other chains where batter is shipped in and just baked at the store.) We didn't sample any muffins or cookies, though.