I just wanted to vouch for MJ Grill on John St., great garlicky Caesar salad. Also, Manon Cafe (Leonidas)has a new outpost near Broadway, and there is a new Vietnamese restaurant. The new Lemongrass on William hasn't been half bad either. All of this in addition to Ise, Sicaffe, Klatch Coffee, Sophie's, Financier Patisserie and the Dean & DeLuca Cafe at Borders adds up to a bunch of choices :-)
What I don't recommend: anything near or within the South Street Seaport. JP Mustard's served me the most disgusting meal EVER (even worse than the worst meal my mother ever served me when I was a kid, and that's saying A LOT). I usually like the chain Cabana but the one over there is extremely unsanitary. I also don't recommend *any* Chinese food over there (Kar, China Grill, etc.). And although I really like Seh Ja Meh's food I won't go back there because they don't allow tables for one.
It looks like a French patisserie is about to open on John or environs, and another fancy restaurant near there.
On another note, although I appreciate Cookie Island, why on earth do they have to put cinnamon in their chocolate chip cookie? For me, it gives the cookie multiple personality disorder...it doesn't know if it wants to be a chocolate-chip cookie or a snickerdoodle.