Eric Eto posted a nice list of Japanese restaurants in NYC to Chowhound recently. The list is copied to my post inside for safekeeping :)
NOTE: I can't seem to control the spacing in this post, so what you see is the name, address, and then the recommended dish, separated by one space.
DOWNTOWN
Omen 113 Thompson ***
Oroblu 333 Hudson Pasta variety ($13.00)
Souen 210 6th Ave Natural Foods ($15.00)
Daikichi Sushi 32 Bway Obento variety ($4.85)
Teriyaki Boy 22 Madison Lane Una-don ($5.99)
Tokyo Lunch 10 John St Japanese food
Tomoe Sushi 172 Thompson Sushi/Sashimi Combo
Nobu 105 Madison St Black cod w/ miso ($15.00)
Honmura-An 170 Mercer Uni-Soba ($18.50)
Yoshi 201 E. Houston Yaki-tori variety ($1.50)
Ajisen 14 Mott St Ajisen Ramen (4.95)
Hoian 135 W. Bway Nama harumaki (spring roll) (7.25)
GREENWICH VILLAGE
Aki 181 W. 4th Mille Feuille (9.00)
ONY 357 6th Ave Menchanko (9.75)
Kotan 121 W 3rd
East 71 University Pl Chocolate Buffet
Jun 9 Barrow Shiokama-yaki (10.00)
Taka 61 Gvove St Special sashimi (28.00)
??? 496 La Guardia Pl Lunch Special (6.75)
Marumi 546 LaGuardia Pl Spicy Sashimi Salad (8.00)
Yama 38-40 Carmine Special sushi roll (7.50)
Zutto 62 Greenwich Ave Spicy Miso Cod (8.00)
Japonica 100 University Pl Maguro tataki teishoku (29.00)
EAST VILLAGE
GO 31 St. Marks Pl Oden set (6.50)
Souen 28 E. 13th Natural food
Sobaya 229 E 9th St Shumai (6.00)
Daikichi Sushi 35 E 8th St Bento variety (4.85)
Typhoon 79 St Marks ??? Bomb (7.00)
Takahachi 85 Avenue A Sushi/Sashimi
Natori 58 St Marks Pl Wani Shoga yaki (5.00)
Hasaki 210 E 9th St Fresh fish (10-20.00)
Bond Street 6 Bond St Sushi Sextet (26.00)
Mie 196 2nd Ave Sushi set (12.00)
Yakiniku West 218 E 9th St. Kalbi set (9.50)
Yakitori Taisho 5 St Marks Pl Yakitori set (12.00+)
Rai Rai Ken 214 E. 10th St Shoyu ramen (6.95)
Lan 56 3rd Ave Special select calf's liver
Sharaku 14 Stuyvesant St New Special Appetizer (7.00)
Shabu-tatsu 216 E. 10th St Ishiyaki Bibimbap (10.75)
Shiki Kitchen 135 1st Ave All foods Tabehodai (17.50)
Sapporo East 245 E 10th St Sapporo Special Ramen
Ave A Sushi 103 Avenue A Dynamite (5.75)
Village Yokocho 6 Stuyvesant St Motsu-Ni
Esashi 32 Avenue A
Ebisu 414 E 9th St Inaniwa Udon (10.00
Otafuku 236 E 9th St Takoyaki (5.00)
Kura Sushi 67 1st Ave Volcano (6.00)
GO 30 St Marks Pl Hiroshima style okonomiyaki (7.00)
UPTOWN
Shabu-Tatsu 1414 York Ave Tokusen (37.50/2 person)
Sushi??? 1143 1st Ave Omakase sushi (35.00+)
??? 1649 2nd Ave Ippin ryori ($4.50)
Daikichi Sushi 1109 Lexington Obento variety
Yuka 1557 2nd Ave Sushi-tabe-hodai (18.00)
Obune 2164 Bway Obune Boat (39.95/4 persons)
???? 2707 Bway (103rd) Sushi Combo (35.00/2 persons)
Teriyaki Boy 483 Columbus Katsu curry (5.50)
Teriyaki Boy 1380 1st Ave Ten-zaru soba (7.00)
Teriyaki Boy 1640 3rd Ave Special chicken combo
Tsuki 1410 1st Ave Tsuki Original Sushi (15.50)
Ajisai 1466 1st Ave Ajisai bento (20.00)
East 354 66th St Sushi (20.00)
EMOÌs Korean 1564 2nd Ave Ishiyaki bibimbap (13.00)
Gajyumaru 1659 2nd Ave Sushi (18.00+)
Kazusa 1400 2nd Ave Kushi-yaki (2.00)
Gari Sushi 402 E 78th Sushi (25.00+)
Kodama 83 1465 3rd Ave Prim
I've frquented Takahachi in the past until I discovered much discomfort and sub-par food. The waiting staff is responsive if you don't get a certain woman server, and the head Chef thinks he's a comedian at the expense of patron's.
With sushi similiar to that at Pathmark, I don't recommend this restaurant even slightly.
A better more reasonable and authentic choice would be Shima's located around 12th street and 1st avenue.