In a nutshell, I would like to suggest Galeries Lafayette Haussmann + Le Printemps, they are next to each other. Le Printemps has just refurbished their niche fragrance section and it's now a fully fledged scent room with a brand new Frederic Malle boutique/corner. The place is very nice and much less crowded than Lafayette.
With a combined visit to Le Printemps and Galeries Lafayette Haussmann you will be able to cover the following niche houses: Frederic Malle, Tom Ford, by Kilian, Creed, L'Artisan Parfumeur, Cartier Les Heures, Histoires de Parfums, Lutens (export line only), Caron, Guerlain exclusives (both Guerlain corners at LP and GL have the Guerlain boutique status so they carry all exclusives), Armani Privé, Annick Goutal, Diptyque, Lubin, Dior exclusives, Aqua di Parma plus some obscure niche French houses.
Needless to say that all the non exclusive fragrances of Hermès, Yves Saint Laurent, Dior, Chanel, Mugler, Kenzo... are available at both stores.
Note that Amouage, Frapin and Parfums d'Empire have just left GL so they are no longer available there.
The good news is that many other great niche houses are all within a walking distance from the Palais Royal / Tuileries area: Lutens exclusives, IUNX at Hotel Costes, Hermes exclusives, Francis Kurkdjian, Chanel exclusives (rue Cambon), Santa Maria Novella (at Amin Kader), Jovoy (Rancé, Grossmith, Technique Indiscrète, Amouage...), Colette (Le Labo, CDG, A Lab On Fire), Nicolai, Lorezo Villoresi, Montale to name but a few.