Wife and I came had an 11-day trip to Japan in April 2013, all in Tokyo and Kyoto. Trying lots of good restaurants was definitely on the agenda. I did a lot of research on websites like chowhound, chuckeats, wanderingepicures, yukari sakamoto, etc.
I have listed my Tokyo places by type (in alpha order by type); I made a separate post for Kyoto. My prices are from memory. I put a ** or * by my top-picks or must-do's.
If a restaurant is reviewed extensively elsewhere on the internet, I won't say much more about it. I'll usually provide a link to the review I found most helpful.
I'm going to do a separate posting for my ramen experience in Tokyo (I tried quite a few).
Curry rice. Moyan.
I read somewhere this was the best curry rice in Tokyo (maybe bento.com?). The curry was way too sweet for me. It doesn't compare at all to Ryokaku in Kyoto. Locals do seem to like it. I got there for the weekend lunch buffet by accident and it was packed with Tokyo locals (we were the only tourists). I guess Tokyo-ites may like their curry rice on the sweet side.
** Depachika. Isetan Shinjuku.
I think this is the best depachika. Great food, reasonable prices, huge selection. You can take your food to the rooftop, which is an oasis and a great place to enjoy your food. To go with your rooftop dining, you can buy sake or wine (a prosecco is a solid value at Yen 2200), or beer from outside. You need to find or bring your own cups.
Depachika. Takashimaya Shinjuku.
This is a very nice depachika but I liked Isetan better. I think part of the high ranking for this one is because of its foreign "brand-name" stalls (like Kayser boulangerie), which I didn't care about.
** Sushi, Top-level. Sushiso Masa.
Fanatastic hi-level sushi!! I'll just link to the ChuckEats ultra-detailed review that got me interested in it.
The fish was top quality, great variety. Fun to watch the master's knifework. Some great dishware.
Our set course was about $220 pp. We had a fair amount of sake and beer and the cost was negligible. One great thing about this place is that the Master Chef himself is very friendly and makes it an overall enjoyable experience, even for non-Japanese. In contrast, some/many master "master-level" restaurants seem to be no fun at all (see reviews of Jiro).
I wanted to try Sawada or Saito (I think they are $400 pp courses) but I couldn't get a res. I think $220 pp is a very fair price (a good value actually) for such an amazing meal. I'd rather spend $220pp at Sushiso Masa than I think any place in NYC that I can think of.
Sushi, Tsukiji. Sushi Dai Bekkan
I really don’t understand why people wait 2-4 hours in line for Dai and Daiwa. I’d rather spend a bit more and go to lunch at a top-level sushi place like Saito. Could someone compare the sushi at Dai or Daiwa to that of a Saito, Sawada or Sushiso Masa? I’m guessing there is no comparison (at least the dinner menu). Maybe its closer vs the lunch menus at the top places?
We bought a box of uni from a vendor inside the main market for $21 and ate it standing among the parked bicycles near the shrine just outside the East exit. It was great! I would recommend just buying a lot of sushi direct from the vendors and eating it somewhere; the sushi looked great.
We went to Dai Bekkan because it was recommended on Yukari Sakamoto's website (useful website). It is not in the main 6-block grouping. It was ok. Filled with Japanese people. If it wasn't in Tsukiji, it wouldn't rate a mention. The color of the banner has changed from that on Yukari's website (think dark blue now) but you can recognize the characters. Also, the store owners there can point you it if you show them the pic.
* Tempura Master. Mikawa Roppongi.
The Zezankyo location is rated higher (the actual master is there) but we couldn't get a res at that location. I love tempura so I was curious to see what top-level tempura is like. It was very nice and I'm glad I did it. Many reviews out there.
* Tonkatsu Master. Maisen.
Fantastic! There are 3-4 grade of pork. I got the [Otoika] Kurabota set, rosu (loin). I wanted to get the top grade but I couldn't tell if the X-set was highest grade or not. In any case, what I was fantastic. I sat at the counter with a view right into the kitchen. Interesting how it is deep-fried in a lower temperature oil. There was no sizzle or smoke.
Many reviews out there. Here's a good one:
A few general notes to help first-time visitors.
1. Most places do not do anything different to cater to foreigner customers; its not they are hostile to foreigners or anything. I would definitely not limit myself to English-friendly places. You can work around it and it will be worth it.
2. Making reservations is crucial for top-level places, as early as possible. I used my hotel concierge for most. It is hard to do directly (most don't speak English). If you make a res, please don't be inconsiderate about cancelling. Inconsiderate cancellation by foreigners is making it hard for foreigners to get reservations.
3. At many places, Japanese beer and sake are the only alcohol options. Few have wine and almost no one has wine by the glass. The upside is that there seems to be no markup on the alcohol they do serve.
4. For location-based searching for restaurants when you are in Tokyo, I found bento.com to be quite useful.