Café Delistar has bagels and is nonsmoking. 3 branches in Munich. Haven't been there yet myself, but am going tomorrow night.
Café Delistar
Amalienstr. 40
Website: Delistar
Tel. (089) 28 99 64 34
Opening hours Mo - Fr 7:30 - 20:00, Sa 8:30 – 17:00