Most travelers to Tokyo would eat at Tempura Tsunahachi down at Shinjuku, just a stone's throw away from Isetan and Mitsukoshi department stores. Of course, the fact that it has been around for about 80 years helps. Also, the fact that locals still faithfully queue, and that prices are reasonable for the quality are probably the real reasons.
Of course, one only eats tempura at Tsunahachi - deep fried in its own secret house blend of oils - available for sale also! There are a variety of sets which have different items (some standard and available all year round while others are seasonal) tempura-ed to Tsunahachi perfection, to be eaten with their 2 types of grated radish (one plain and one infused with umeboshi) which you can drown with the tempura dipping sauce, a bowl of steamed rice, pickles and of course, miso soup with tiny clams.
Today, I had the Y2770 set which had 2 shrimps, cuttlefish, eggplant, a tempura pancake topped with many shrimp, and the seasonal clam with julienned ginger/mushrooms as well as a pond smelt and conger eel.
Great value and of course, great quality!
Caution: do not wear clothes you intend to wear again - reason: YOU CAN'T (unless you want to smell like tempura)!
3-31-8 Shinjuku, Shinjuku-kuTokyo, Japan
* Many locations around Japan, with 8 in Tokyo alone