42!!!I think Le Bernardin is generally accepted as "the best" but (unfortunately for me) I've never been there.
There are simply so many places to eat in Manhattan, not to mention the rest of the boros (and they SHOULD be mentioned, because some great food is in every one of them!) that I couldn't begin to recommend. A simple "best pizza" discussion here can start a fight; thin crust, thick crust, artisan...
Some places are iconic for their locations, therefore worth it for an interested visitor (e.g. The Rainbow Room, The River Cafe.) Other places are cult-ish, either super-trendy or closed-circle and almost no one can get in (e.g. momofuku, Rao's.)
If you're here, don't discount street food, much of it these days is excellent. It's an entire sub-culture.
The 'net is loaded with guides, with the dawn of food TV, celebrity chefs, etc. there has never been a time like now for culinary tourism and foodie pursuits. We've even got multiple distilleries and breweries back up and running. They do tours and tastings too.
One rule I can comfortably offer: There is no reason to eat in a chain restaurant in the City of New York.
Follow that tip, skip the obvious tourist traps, and you'll find something good. Let me know, I'll make our reservation!