AFAICR, there are 4 yakitori restaurants in the latest Michelin guide:
Birdland in Ginza
Yoshicho in Gotanda
Takahashi in Gotanda
and Toriki in Kinshicho

I've not been to Toriki, but all the others were excellent in their own way.
Takahashi was noteworthy in that the chef used to run a French restaurant and offers a good selection of wine, including a special Cote du Rhone cuvee bottled especially for him. It also has a nice contemporary ambiance. Recommended, although not exactly on the beaten track.

Another old favorite is Bird Court, out in Kita-Senju.

I think the actual name is Kanaiya かな井屋:
http://r.tabelog.com/tokyo/A1309/A130...
It specializes in dishes like stamina-horumon-yaki, mostu-nabe and the like.

The new (or rather soon-to-open) Keisei Sky Access line might offer a better and faster option for getting into the city. It's due to go into service on July 17 this year.
I haven't seen any timetables for it, but it's supposed to link the airport with Nippori in just 36 minutes.
So it might be worth coming back to this thread in the summer, when the options will clearer.

More info here: http://en.wikipedia.org/wiki/Keisei_N...

Kami-noge is just down the road. If you feel unagi might hit the comfort food spot, then try Kikukawa:
http://search.japantimes.co.jp/cgi-bi...

But it does now (as of Saturday) in Yokohama, in the Red Brick warehouse. Open from 9 am and very nice too.
http://r.tabelog.com/kanagawa/A1401/A...

Great report.
To my knowledge, Bird Land was the first yakitoriya to offer pate, and it's always been excellent. Also probably one of the first to offer a range of wine and imported beers -- so it's quite likely that chef Wada uses cognac.

According to tabelog, Kissou is closed on Sundays and (all) Wednesdays.

I think the OP was referring to this Robata:
http://www.sunnypages.jp/travel_guide/tokyo_restaurants/izakaya/Robata+Honten/421
It's a funky old place that's been around for decades (it's also pricier than it looks, this being Hibiya). But the food is not that great and certainly not essential for a brief Tokyo visit.

Bird Land (two words) would be a fine place to hit the ground running on your first evening. And since they got into Michelin they have their own web site and you can handle the reservations yourself online:
http://ginza-birdland.sakura.ne.jp/re...

Well, for whale the obvious place to start might be Kujira-ya in Shibuya (right below the 109 Store). It serves full course meals of various kinds of kujira (= whale).
Here's the url: http://www.kujiraya.co.jp/
Here's a map in English: www.tradina.com/0334619145/map.html

However, for a much more atmospheric evening with plenty of good sake (especially Uragasumi), there's Taruichi in Kabukicho (Shinjuku). It's not that easy to find but worth the search. Here's a map (also a coupon for a free beer):
http://r.gnavi.co.jp/fl/en/g362300/coupon.htm

As for fugu, there's too much choice: one option that's central might be Genpin-fugu, which is down the side street next to Midtown. The look is pretty modern/cool, with lots of tanks of live fish. Here's a map (plus coupon for a free serving of kara-age) in Japanese:
http://r.gnavi.co.jp/g254270/map1.htm

Also in Roppongi but more traditional and much pricier (¥3-40,000/head -- and remember cash only!) is Ajiman (now with a Michelin star to its name).
Lunch is affordable though:
www.tradina.com/0334082910/

Interesting. It seems Ueki is weaving quite a few Japanese ingredients into his cuisine. And you can't get much harder-core Japanese than shirako (cod milt) which sounds like what you had.
Some friends are going to try out the same combi of regulat/veggie that you had.

glad to hear that.
out of interest, which of your dishes were less successful? Any stand out as great?

I should add that Ueki and his wife (who is often on the front desk) both speak good English.
As for price, the 9,500 yen course was fantastic. My wife (we were there for her birthday) had the ¥6,500 course and that was not quite as complex, but still lots of beautifully presented dishes.
Also, if they know it's your anniversary, they will probably prepare something a bit special for you (as they did for my wife).

When we ate there in the spring, the menu was (IIRC) ¥16,000. By the time everything was added on (couple of tokkuri of sake; ceremonial matcha at the end) the total was ¥52,000 for two. It was very good and visually stunning, but it's a small place with just a single counter and it really depends who how discreet (or boisterous, as in our case) your neighbors are.

Here's a place I can recommend highly: the new (or rather newly reopened) Restaurant J in Hiroo.

The chef, Ueki, cooks a very modern, Japanese take on French cuisine, using a variety of local ingredients (miso, yuba, etc) featuring an amazing array of vegetables throughout — even as far as the desserts.

The regular menus are not vegetarian, but there is a vegetarian lunch plate and Ueki told us he is happy to prepare fully vegetarian multi-course meals if he's given enough advance notice (a few days). He's a very good chef, and I'm sure he would make it look very special.

The original Restaurant J (which served more Pacific Rim style cuisine) closed 4-5 years ago. The new incarnation has only been open about a month, so there's not much of a buzz yet. But it's good enough for at least one Michelin star based on the great meal we had there, one of the best we've had in recent months in Tokyo.

Here's the url: http://www.msinter.co.jp/j/menu.asp