Doughnut Plant (NYC) is amazing. My faves are their creme brulee doughseed and dulce de leche cake donuts. My work was closing up our desk in SF and relocating to NYC and it was DPlant that convinced me to move.
Dough (NYC) donuts are also amazing. I feel like their yeast donuts are better than the yeast donuts at Dplant.
Underwest Donuts (NYC). It's inside a carwash.
Doughnut Vault (Chi) old fashioneds are really amazing too.