Tabelog is used by most people. Almost all restaurants are on there and you can get info on restaurants, see reviews and pics. Essential info such as whether they take single diners, credit card, … are also on there. On the Japanese site, you can also search by type of food, location, ranking, …
For in-depth discussions, tokyotabletrip is also good for English speakers
Other than those, not many sites that are very useful. A lot of the people who travel to Japan are on Instagram so you can always see where these people go
