There are many, but here is my short list:
Butchers: Desnoyer (www.regalez-vous.com) in the 14th is the provider of the best restaurants, Boucheries Nivernaises (for their Bavarian beef, well aged) rue du faubourg saint honore, le coq saint honore (two stores one next to the marche saint honore, the other in the rue des martyrs) for nice fowl but not only, lesourd rue lecourbe.
Very fresh fish: Christophe, in the market of Passy, in the corner most opposite to the entry -- exceptional fish and exceptional work on it. Chrono peche has been renamed but still has a concept of hyper fresh fish, with shops in the rue des martyrs, next to the place Victor Hugo and rue Tocqueville. Fish shop rue Mouton-Duvernet a great professional too. Of course la poissonerie du Dome, though it is a bit overrated and overexpensive imo. There are many good fish shops, but very few with exceptionally fresh fish.
Choosing fresh fish is easy: it always shows how fresh it is, cause it must be firm, without smell, shiny eye. And the thing that is harder to see (whether it is from farm or fish) they ususally write, or at least tell.
And in general, just like any food shop in France, ask what is particularly good today, and leave if they tell you everything is.