[chief_]

The absolute best places to get Japanese food are in Porter Square or Brookline IMHO

Porter Square -- Bluefin, located inside the Porter Exchange Mall (basically a mid-size Japanese mall filled with other various restaurants and some department stores), food is very good and reasonably priced, atmosphere is laid back.
The owners and servers are Japanese and the service is quite excellent.

Brookline-- Fugakyu. More expensive than Bluefin and nicer ambience, food is probably about as good. Huge restaurant, if you do decide to go here over Bluefin I suggest getting seated in one of the "sliding door rooms" on the first floor near the koi fish pond or at the upper far left area of the restaurant (the blue area)

Bluefin it's pretty easy to get seated (you don't need reservations) whereas you pretty much need reservations for Fugakyu.