The two main Japanese food stores in the area are both in Cambridge - Kotobukiya in Porter Square and Yoshinoya off of Central Square. However - several Korean stores carry a significant amount of Japanese ingredients. The questioner noted Shin Shin in Lawrence and that's ok and getting better all the time (esp since they added the butcher/fishmonger), but the Republic Market in Union Square in Somerville really has just about everything Japanese you'd want, including a decent sake collection. I get much of what I need at Shin Shin and the Chinese grocer in Chelmsford, but I do periodicaly have to run into town to get certain items I can't get at the Korean store. I also mail order a lot - the best miso around is made in western Mass at South River Miso (link below). The best natto is also made by a different group of folks in western Ma.