The produce and meat/fish in standard supermarkets in NYC seems pretty bad, and expensive to boot. Of course, we could always shop at a specialty store, but my wife and I are looking instead for places we can buy our groceries more directly from the source. So far, we've found two:
Stiles Farmers Market @ 42nd and 9th. Very inexpensive produce, though selection is limited and quality can vary (though in no case worse than places like Gristedes). Excellent butcher shop, with good range of cuts at very reasonable prices. The attached grocery store also sells packaged goods, at prices about 5% below Gristedes.
Sea Breeze fishmonger at 41st and 9th. Excellent fish (though not the living swimming stuff you can see in Chinatown). Very reasonable prices. Last week we bought 2 lbs of great, fresh tuna for $7/lb.
Any other recommendations?