Chain: it's Jimmy Johns hands down. #12 (the Beach Club) sans Cucumbers and Tomatoes every time.
Local: Although I no longer live Boston, my favorite place there was Ideal Sub Shop on Dudley Street near DSNI (Dorchester/Roxbury). I used to work at a school nearby when I did Americorps and we'd go there all the time! Cheapest and best I've ever had. Nothing in St. Louis comes close! Everytime I go visit friends, even though it takes forever to get there--we still go