Fast and Fresh deli is NOT cozy. It is a great chowhoundy find, but not the Boerum Hill experience. the jewelery/clothes/linens shop next door is terrific if you are a lady, or shopping for one.
I second the vote for Building on Bond. It's good for a coffee stop too.
Rothchild's on Atlantic is also sweet.
Mile End is cozy and delightful, but there is a wait if you show up after 10. Get the hash. Actually, get anything -- the food is amazing.
If you visit on Sunday, there is an indoor farmers market on Atlantic.
Building on Bond
112 Bond St, Brooklyn, NY 11217
97 Hoyt St, Brooklyn, NY 11217
411 Atlantic Ave, Brooklyn, NY 11217