I came to this late and it sounds as though there are some great recommendations here. It’s always a question whether Lleechef or I will be the first to recommend Daily Catch. For style of food, it is Sicilian seafood. Mostly garlicky with a lot of tomato-based dishes, but each dish is prepared individually (i.e. the red sauce with the mussels is different from that with scallops or shrimp). The fried calimari is the best, anywhere. If you want a real assertive pasta dish, I like their homemade black pasta aglio y olio, with ground squid in the sauce. I believe the North End location is still cash only. It’s also tiny with an open kitchen, and many of the dishes are served in the pan they’re cooked in.
Another I’d highly recommend is LaMorra, sort of off the beaten path on Route 9 (Boylston St.) in Brookline Village (like most things in Boston, it’s easy to find if you know where it is). It is Italian, but the chef has studied old Tuscan cooking and comes up with some very unusual dishes. Don’t miss some of the little starters like fried olives and the meatballs. The first course of risotto with marrow and red wine is heaven.
Add. – noticed that you mentioned that your Wife is sensitive to bad neighborhoods. Be advised the Berezka is in Allston, which sort of poses as a bad neighborhood for the benefit of college students.
Also, thought of one more of our favorites that is way off the popular radar. Jasmine Bistro in Brighton Center (there’s a municipal lot next door on Market Street) is a Mom, Pop and family run Afghan/Hungarian and French place with some Indian. Service is old world and friendly and the food is a choice among goulashes, curries and traditional French, all done beautifully. My BIL who spends every weekend and lots of cash on South Beach was amazed.