Surprised no one has mentioned Kee's Chocolates. She has several stores, the original in SoHo, and two in midtown. Unusual flavors, excellent ganache, high quality overall. She also has macaroons, though I haven't tried them and don't want to wade into the current debate about the best ones in New York.
Kees Chocolates
Christopher Elbow, based in Kansas City (of all places!) also makes excellent truffles and ganache-filled pieces. They are available at Dean & Deluca at 1150 Madison. Given that D&D is outrageously expensive, be prepared to pay through the nose.
The original Payard on 3rd was excellent; I find their latest incarnations to be much less compelling. Neuhaus, Godiva, etc are plebian. Useful in a pinch, otherwise not worth the price.
If you want chocolate bars and other chocolate confections, you can try The Meadow at 525 Hudson. Lots of superb bars and unusual gifts. Supposed to have wonderful flowers, too, but again I cannot vouch for them.
The Meadow