Apero Wine Bar [Aoyama]
This place is beautiful! It has large window walls from which you get a peaceful view of the townscape; it's decorated stylishly and has changing ikebana ornaments as a centrepiece. If it were just for the ambiance it would be worth going, but on top of that, it serves some organic foods (french bistro style appetizers mostly) and really fine wines. Wines are a bit on the pricey side (¥1,500 for a glass and ¥5,000 for a bottle). It's the ideal spot for a date or spending some quality time with some friends.
You can go there for a Sunday brunch as well. It's located at a 6-minute walk from the Gaienmae station or a 9-minute walk from the Omotesando station.
Vin de Reve [Ginza]
This Ginza wine bar is a little gem that serves over 100 kinds of fine wines and French cuisine made from organically produced vegetables. The selection of the foods and wines changes with the season so just ask for recommendations at the time you go. They have an abundance of items you can order a la carte and they also have courses that are between ¥6,800 and ¥8,700. For the quality, the prices are quite reasonable. Plenty of food items are below ¥3,000.
Ginza Kakutei 銀座 六覺燈 [Ginza]
This place is the best for some Japanese fusion cuisine paired with wines! Their specialty is kushi-age (deep-fried skewers), which is an authentic Japanese kind of cuisine, but theirs are made with Chinese and Western ingredients as well as Japanese. The result is really good! They go amazingly well with wine, but also Japanese sake and spirits. So there's a little bit of everything for everyone here. For great wine and some of the most original kushi-age in Tokyo, this place is worth the detour.
Tsubaki [Azabujuban, Roppongi]
Tsubaki is a French high-end wine bar and restaurant. The wine selection is just as impressive as the quality of the food they serve. The in-house sommelier may recommend the best pairing for the meal you want to order. Since this is a high-end restaurant - and one of the best of its genre in Tokyo! - you should expect to pay over ¥10,000. Their fish cuisine is particularly good.
Located at a walking distance of the Roppongi or Hiro stations.
lumielune [Shimo-Kitazawa, Higashi-Kitazawa]
Lumielune is a bar that opened in 2014 but that has a rustic interior. Note that it's a non-smoking bar, which is somewhat still rare in Tokyo (there's an area outside for smoking, however). Their specialty is wine, but they also serve some really original dishes that are so beautifully presented, often having plenty of seasonal references such as sakura petals or other flowers that are in bloom at the time. The place has a quiet and cozy ambiance.
You can get there from the Shimo-Kitazawa station (8 minutes by foot) or from the Higashi-Kitazawa station (about 3 minutes).