First-timers at the Brooklyn Bagel Bakery, a squat factory in a part of town now better known for burritos and Filipino sinigiang, are often put off by the display in the cramped retail vestibule, glass cases full of blueberry bagels and strawberry bagels, cranberry bagels and chocolate bagels, banana-nut bagels and other affronts to the proud tradition Brooklyn Bagel has been carrying on since Sandy Koufax still pitched in his native borough. The most crowded bin is the one holding the puffy, blown-out, over-sweetened plain bagels more or less identical to the ones at suburban bagelries. Has Brooklyn Bagel sold out? Posterity will have to decide. But the signature product survives here as Hearth-Baked Bagels — just another flavor here perhaps, like pumpernickel or jalapeño cheese, but these plain bagels are dense, chewy, taut-skinned and properly boiled before baking. They are still the best bagels west of the Hudson.