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Personal Favorites:

Brooklyn: Montague Street Bagels
Manhattan: Ess-a-Bagel

Favorite used to be Bagel Zone (Ave A between 3rd St & 4th St), until they changed their name and stopped baking their own. Was the perfect bagel -- crisp on the outside, soft and bready on the inside...I'd pay a ridiculous premium just to taste one again.

I understand the scientific urge to use the plain bagel as one litmus, but that just aint the whole tale of the taste. And I don't get the animus all the tasters apparently have against size, especially in the rising-price world, if the maker can deliver all the qualities of outer crunch, inner chew, and flavor balance. What, we want a LITTLE bagel? Hard to take that seriously. If you can experience the fresh pumpernickel at Ess-A-Bagel and not immediately comprehend how the combination of rye-and-carraway tartness and the kiss of malt create a tension that is absolutely thrilling--the single greatest bagel experience in NY--then you aren't paying attention. This is an art object. I live down the block from Rolen and Bagel Corner in Riverdale, and every weekend I travel down to 20th and First; there isn't even a serious comparison. Incidentally, Ess-A-Bagel appears, uncredited, in the poem "Creed" by contemporary poet Meg Kearney--to my knowledge, though they have satisfied many writers and appear as props in literature , these are the only bagels actually to be celebrated in a serious work. Here's the link: http://www.megkearney.com/creed.html

@Anapowell try any of the above with the exception of Lender's or Dunkin. They are all better than La Bagel.

"Please put to rest immediately the myth that Montreal bagels are superior to New York City bagels"

http://www.seriouseats.com/talk/2007/03/montreal-bagels-exposed.html

http://chowhound.chow.com/topics/653172
--Guttergourmet

I think the theory of a bagel expiration taste time is a valid one. I've always been a huge fan of a small place called Bakers Dozen's out in Kew Gardens Queens. They make them there right in your face and have a 6dollar/dozen deal... but you know what, I lived less than a block away from the place so its no wonder the bagels I bought from there were extremely fresh and tasty. I still take the trek out there sometimes to get my fix.

http://www.yelp.com/biz/bakers-dozen-bagels-kew-gardens

Here is a link to an interesting web page about the famous Watson Bagel bakery in Essex Co., NJ.
I literally teethed on these bagels as a baby, and some of my earliest memories are of my father taking me there late at night. We would buy a bag of hot salt bagels for 7¢ each, and eat them in the car on the way home, just as soon as they cooled off enough to touch.
The illuminated doorway of the store was like a beacon in the dark, open all night when all the other neighborhood businesses were closed. I remember the worn, wood plank floors, the big baskets of golden bagels sprinkled with gleaming white salt, and the wonderful, warm aroma that permeated the place.
http://www.oldnewark.com/memories/weequahic/bodianbagel.htm

I have to agree that Daniel's bagels in Murray Hill is my favorite, despite living across the street from Essabagel on 1st and 21st for 7 years.

I also happen to love Cropsey Bagel near Coney Island, and Bagel Boy in Bay Ridge. Getting them hot and fresh is the only option for me, I will not toast a bagel.

Bagel Hole is the best bagel.
Most of the others are oversized and underbaked.
Another great bagel can be gotten at Boro Park Bagels,
4305 14th Avenue, Brooklyn.

At last! Recognition for Brooklyn Bagel! There's no comparison. :) I have been known to walk there in pajamas for a mini everything bagel with cream cheese.

Also--you couldn't ask for a sweeter band of bagel guys.

Yeah!!! I love the Bagel Hole. It has the best bagels I have ever eaten, and I've lived in Brooklyn for most of my nearly 5 decades, and have eaten some very good bagels from some very good and now extinct bagel stores.. I'm always worried it will go out of business, because it is small and unassuming, and is merely a bagel store, not a huge deli -- and because I am fatalistic and assume that the forces of darkness too often triumph. But maybe in this instance virtue - in the form of amazing delicious old-fashioned bagels - will win out over glitz and marketing and fame.

@uncajay & @NYminknit: I think Carey did a fine job with this post, regardless of her state of origin. She has a good palate, is discerning and passionate about food, and is a great writer/blogger/editor, which is why we hired her. I had several LOL moments reading this, particularly her clever "Heisen-bagel Uncertainty Principle."

@dmcavanagh
Yes, and I would also suggest using the malted barley syrup in the water too (enough to make it look like strong tea), rather than using baking soda as he suggests. The results, I find, are better. Also, many swear by the bagels in Hammelman's BREAD over Reinhart's, although really, both are excellent. I have found that these recipes allow me to make a better or at least equal bagel compared to just about any of the places listed above.