Bay area has a lot of good Japanese eateries. You do not need to visit VC to have fresh seafood:) I will start with couple at south bay. Hopefully, someone else can add some that I do not know.
Ramen:
Santouka, inside a Japanese market. Rich broth, QQ noodle, pork cheek meat.
Sushi:
SAWA - Omakasa - best fish and big-ego chef. you have to listen to his dry-humor.
Kapaa Nami Nami - good mixture of regular and special dishes
Izakaya:
Dan Izakaya - authentic, very good small plates