I also just got back from a trip to Boston, and enjoyed the following places:

-- Tapeo (Newbury St.): Spanish tapas and big dishes like paella valenciana, all authentic. The main dishes are pricey, but you can order paella for two (believe me, there's plenty).

-- Stephanie's (Newbury St.): Great lunch place with patio for watching the street scene. Food's quite good and not too expensive.

-- Antico Forno (North End): Italian, of course, but just a bit different from most of the North End places. Tight quarters, but great food. Also reasonably-priced.

-- Skipjack's (Back Bay on Clarendon): Seafood. Not horribly expensive and quite delicious food.

Boston is not a cheap city as far as food goes, but what the hey, you're on holiday, right?