I'm an NYC boy who grew up 3 blocks from H & H and Zabars. To be honest, "Ess a Bagel" in NYC downtown is my winner for NYC bagel.
For Boston... if you start out at Kupel's for bagels then head towards Brighton on Harvard Street and stop on Comm. Ave., "Berezka" the Russian place has excellent smoked salmon, lox, whitefish, sturgeon, sable, etc! All sorts of gourmet foods.
That combo is up there with the H & H / Zabar's combo in my book.
One additional note, quite a few of my Russian friends prefer the Russian Grocery on Beacon Street and Washington, forgot the name. If you make it up there don't miss the Greek/Parisian Bakery on the corner nearby. Really excellent cakes and pastries.