not really a coffee shop but they have a discount for nyu students and a bagel + coffee are $5 so pretty affordable (for nyc) :) i went there every morning before class!
Heavenly Finest Deli
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nice people & comfortable location especially for coffee chats before/ after class.
Third Rail Coffee
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tastes amazing & meal exchange is possible (i found that out way too late)
Peet's Coffee - NYU
bagel shops
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may be crowded but worth the wait :)
Apollo Bagels: HOME
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probably the best bagels i had & aesthetic look :)