Lemon-Poppy Seed Muffins
Two Little Red Hens has good homemade-style muffins, and perhaps they have lemon or almond poppy seed.
Then there's Wonderfoods on 36th and Fifth, whose muffins are more commercial - but as a muffin junkie, they fill the bill. Dunno if they have lemon or almond poppy seed but they have quite an array of flavors. I like the Awesome Crumb. Kinda plain, but good to me.
Dean and Deluca also has an incredible selection of muffins, brought in from around the city (both at the front counter and back with the breads). Perhaps if you ask the manager he or she might be able to help you track down what you are looking for.