1) La Maison du Macaron (Chelsea neighborhood in NYC) - Love the atmosphere here. They have delicious macarons in a variety of flavors that goes great with their cappuccino. The comfortable seating in the back allows you to enjoy every morsel of this delicate sweets.
2) Bouchon Bakery (Midtown neighborhood in NYC) - I love the quiche here and their French macarons are another thing to love at Bouchon. It has that crunch and chewiness that makes a great macaron. The place does get pretty crowded, so I recommend getting the macarons to go and find a great spot at the park and enjoy it there. They also have locations in Yountville and Las Vegas.
3) Miette (San Francisco) - Miette has several locations in San Francisco but my favorite one is their Hayes Valley location. This place just oozes with cuteness! You walk in and you get immediately drawn to the pink and green pastel colors of the shop. The macarons are so delicious that it truly is the star of the pastry shop. Miette is offering a Father's Day special. Check out GiltCitySF.
4) Cocola Bakery (San Francisco Bay Area) - Cocola has several locations in the Bay Area. The one I've been to is their Santana Row location in San Jose. This place is alwasy crowded for a reason. Their pastries and cakes are delicious! My two favorites here are their macarons and the Le Sultan (Hazelnut Cake).
Images via Miette, La Maison du Macaron, here, and here