Each area is different I guess. In NYC Whole Foods is among the cheapest of the supermarkets and one of the highest in quality. For example, Gristedes and Morton Williams cost more and their fruits/veges selection is poor.
I think you mean Manhattan, the other boroughs have a few more options like Waldbaums and Key Food, etc.
Manhattan sucks for decent affordable groceries because there's a substantial culture of frequently eating out and those that eat in normally do so because they want the gourmet experience at home, so they're looking for high-end stuff. That and everything costs more in Manhattan.
Go across the river to NJ and right away you'll see Wholefoods is obscenely expensive when compared to Trader Joe's, H Mart, Pathmark, Shop Rite, and local farmers markets.
Manhattan sucks for decent affordable groceries because semitrailers, are not permitted in most of the city. Everything has to be transferred to smaller trucks, which usually means a pass through, and possibly resale at, the Hunts Point Food Distribution Center in the Bronx, or through some facility in New Jersey. In many parts of Manhattan, trucks aren't allowed at all during the daytime. So there's lots of extra handling required.
Yes, but there are only 3 Trader Joe's in all of Manhattan. Two of them are down near NYU and the other is on the Upper West side, which makes them difficult to access for people living in midtown, uptown and virtually the entire east side.
On the upper east side, where I live, the options are pretty much Gristedes, Morton Williams, Food Emporium and Fairway. Gristedes and Morton Williams are overpriced with a bad selection of produce. Food Emporium is worse. Fairway's prices are more reasonable and the produce selection is actually quite good, but I tend to think the quality of Whole Foods' produce is a bit better.
Except I've found the produce in the small corner grocery stores (like Associated's) to be much lower cost and the same or higher quality (due to the turnover).