Nearly three years after opening in downtown San Francisco, Shorty Goldstein’s Jewish delicatessen finally has what owner-chef Michael Siegel is calling “the last piece of the puzzle” — its own housemade bagels.

And these aren’t just any bagels. I’m declaring them the best in the Bay Area.

“Since we started making our own rye [in July 2013, three months after opening], we’ve pretty much been making everything in-house — down to our own mustard and ketchup,” Siegel said. “Now, we officially make everything ourselves. The last piece of the puzzle was bagels, and we’ve always been game-planning when that could happen.”

It happened just last month as Shorty’s — open for breakfast and lunch on weekdays only — started cranking out about 40 New York-style bagels per day: plain, onion, sesame seed, poppy seed, sea salt and everything. The cost is $2 per bagel; $3 with plain cream cheese or $4 with flavored cream cheese.“As we get more comfortable with the process and I feel we can handle it, I’ll start playing around with some other flavors,” said Siegel, whose workday starts at 4:30 a.m. “One of my all-time favorites is pumpernickel, so that’s something I’d like to do.”

Shorty’s bagels actually have been available since September, when a monthly pop-up farmers market began at the Yard at Mission Rock (across from AT&T Park). The series will conclude its current run on Sunday, Dec. 20 from 10 a.m. to 2 p.m., and Shorty’s will be there.

Siegel spent about three months perfecting his bagel recipe, then used the Yard as a testing ground. He uses a local flour (Guisto’s) and hand rolls the bagels, then proofs them for 24 hours before boiling and baking. “The recipe is actually simple. It’s the process that gets super tricky,” Siegel said. “If you boil them too long, or if you overproof them, you get a bagel that isn’t right.”

One genius twist is Shorty’s onion bagel. Noticing that onions on a bagel would often burn in the oven, Siegel decided to incorporate bits of onion into the dough. The result is amazing, with a thick onion taste throughout. It also solves the problem of the bottom half of a standard onion bagel not having much, if any, oniony flavor.

The onion is my favorite. But all the bagels have an excellent crunch-to-interior ratio, with a super crispy crust and a firm, extremely chewy interior — so good that you can enjoy one without putting anything on it. The bagels have a cornmeal bottom, with pockmarks on the crust. And they’re not uniform in shape, which adds to the experience, in my opinion. More important, the flavors really shine. No toasting needed, of course; if a bagel needs toasting, fughettaboutit.

Shorty’s used to serve bagels from Baron Baking in the East Bay — a quality product that’s now available at several Whole Foods locations — but Siegel’s new creations are a tad better.

The first ones start coming out of the oven shortly before the doors open at 8 a.m. With only a few dozen available each day, get there early. Shorty’s won’t sell more than six to any walk-in customer, though bulk orders are accepted 24 or more hours in advance.

Shorty Goldstein’s

126 Sutter St., San Francisco

Monday-Friday 8 a.m. to 3:30 p.m.

(415) 986-2676

www.shortygoldsteins.com

SHEGETZ STILL HOT: Three-month-old Shegetz Bagel (www.shegetzbagel.com) is still going strong with twice-a-month Sunday morning pop-ups at PizzaHacker on the Bernal Heights stretch of Mission Street in San Francisco. The long lines have dissipated somewhat, as preordering has become popular.

The pop-up’s calling cards are hand-rolled, boiled-and-baked bagels served right out of the oven (the promise is “from the oven to the customer in 30 minutes or less”) and super-tasty topping combinations such as smoked trout with cream cheese, dill, creme fraiche, shallots and capers.

That particular menu item is called “The Fussy Rabbi,” and it’s what I tried on my first visit — finally! — to Shegetz on Dec. 13. It was delicious and worth the $10 price. Other menu items include smoked salmon and sturgeon, and whipped Humboldt Fog goat cheese rather than cream cheese. Bagel options are plain, sesame seed, poppy seed and everything.

Hot, or at least warm, out of the oven, the bagels are excellent. But I’d venture to say that any bagel fresh out of the oven (even a Noah’s, for crying out loud) would score higher than it would a few hours later. Truthfully, aside from the everything, Shegetz’s bagels aren’t super tasty on their own. But they do have a nice crunch, a tender interior and are very seedy. And they certainly do sing with their freshness and those toppings. Ben Kaminsky, one of Shegetz’s three operators, said their bagels are still a work in progress to some extent.

Kaminsky also said that even though Shegetz has been incorporated, the plan for the time being is to continue as a pop-up. “We will definitely talk to people that want to invest,” he said. If money does come in, a brick-and-mortar location could be in Shegetz’s future.

EVEN MORE BAGELS: Neither Shorty Goldstein’s nor the tasty bagels at Bom Dia Market were mentioned in the solid San Francisco Chronicle food section piece “Is the Bay Area developing its own style of bagel?” (sfchron.cl/1QU46Wk).

The article focused on San Francisco and gave a tip of the cap to many places, so it’s too bad Bom Dia, a year-old, upscale corner market in Noe Valley, didn’t get mentioned. The market (www.bomdiamarket.com) offers a total of only 12 to 18 bagels each day, made in its kitchen in the Mission District. The varieties are salt, multicolored sesame seeds, poppy seed and za’atar.

I recently tried the latter two, and my taste buds really enjoyed the experience, especially the one topped with za’atar (a Middle Eastern herb). The crust isn’t crunchy enough, but the middle is soft and chewy and has a good consistency. They also have some good heft and plentiful seeds.

The Chronicle piece did give plaudits to some of my other favorites: 20th Century Cafe in Hayes Valley, Marla Bakery in the Outer Richmond, Sour Flour in the Mission, Authentic Bagel Company in Oakland and Shegetz. It also gave some ink to Wise Sons Deli, which still hasn’t started making its own bagels yet but hopes to do so before the end of the month. The piece also failed to mention House of Bagels on Geary Boulevard, which I really like and which often gets overlooked.

Leftovers …

The Eat-Drink-Play food blog in the San Jose Mercury News had an item last week about the new Tiberias Grill in Sunnyvale, noting that the owner, Meir Nahum, is from Tiberias, on the shore of Israel’s Sea of Galilee. The restaurant opened earlier this month, but its website (www.tiberiasgrill.com) now notes that it is closed and will reopen on Dec. 21. Its specialties, cooked on an open charcoal grill, include pagiyot (chicken thighs), levavot (chicken hearts) and shashlik (beef skewers), each served in or with a pita or on a round flatbread called lafa … Here’s another new local spot with ties to Israel: Village Hummus in San Mateo. Open since late August, it’s owned by kibbutz-raised Mike Lewis and his wife, Dalit. Lewis says it’s a “simple concept,” with hummus bowls, schwarma and schnitzel, but it’s apparently working: There are more than 65 reviews on Yelp, and in a rare occurrence for so many reviews, the aggregate rating is a perfect five stars (www.tinyurl.com/village-hummus). One Jewish community insider told me the hummus is “better than Oren’s” in Palo Alto … Local Mission Eatery, which received a lot of plaudits for its devotion to using only local ingredients when it opened in San Francisco in 2010, is closing its doors on Dec. 19. The restaurant is owned by Yarom Milgrom, who is the son of a rabbi and a student of Kabbalah whom J. featured in 2010 (www.jweekly.com/article/full/57981) … Goodman’s Jewish Deli, a farmers market favorite in Sonoma County, is on hiatus for the winter, but operators Les and Tara Goodman went out with a bang: four nights in November and December when they served up their meshuga fries and other Jewish favorites at St. Florian’s Brewery in Windsor. Les hopes to return there and has other plans, as well, such as expanding the stand’s Sephardic offerings (which have been a hit), staging a few pop-ups and teaching cooking classes (one Ashkenazi-focused, the other Sephardic) next month at Congregation Shomrei Torah in Santa Rosa. For details on it all, stay tuned to www.facebook.com/goodmansjewishdeli.