DOMS in Little Italy is super. It is an experience that is utterly unique and charming.
Also, Legal Seafood for fish -- excellent quality and mid priced. Lobsta..and their clam chowda is the best
I also like Fanueil Hall for lunch...that area is super and all the fast food is WONDERFUL..specially the lobsters to go and the clams with bellies.
I lived and worked there and these are my favorite places.