Snuggled between beautiful colonial-style homes and nestled behind a bamboo forest, Restaurante Nagaoka IS the best Japanese restaurant in Mexico City. Given its number two rating on Trip Advisor, it seems many a tourist trek down to Colonia Napoles from the city center for an authentic Japanese meal in the land of tacos. Having lived in Japan, I was a bit skeptical how good Japanese food could be (even many large US cities fail horribly at Japanese cuisine). I guess Mexicans like it, but most of the rolls I've eaten in Mexico City have cream cheese, a damn shame for Japanese food.
So we decided to head down for lunch, as the reviews we read said dinner time was crowded and required reservations. We sampled a little of everything--sunomono, gyoza, shishamo, sushi, and tempura--and my only complaint was that the tempura came to me soggy and slightly cold. For a mere 150 pesos ($12) per person, Restaurante Nagaoka has won me over! The ingredients are authentic, the sauces are subtle, and I spotted no cream cheese in anything I ordered.
If you take public transportation, take the Metrobus to the Poliforum stop. Cross over to the west side of the street and turn right at Arkansas. If you drive and are coming from downtown, go south on Insurgentes, and turn right at Arkansas. The restaurant will be on your left, behind the bamboo forest.
P.S. If you can't make it down to Napoles, another lovely, lovely, option on the weekends that I just can't get enough is the outdoor grill at Mikasa, a Japanese grocer in Colonia Roma. On Saturdays and Sundays from around 12-3pm, Mikasa sells grilled goodies--takoyaki (octopus balls), yakitori (grilled chicken skewers), onigiri (rice balls), and more! Too many delectable treats to name and only about 10-20 pesos for most items. Grab a can of Sapporo from the store inside, pull up a chair at their outdoor patio, and stuff your face like I do knowing that you'll have to wait another week for their grill to open up.