The best omakase I have had is at the bar of Sushi Nakazawa with most of the 21 pieces of nigiri served by Chef Daisuke Nakazawa, himself for $150. If you choose to dine at one of the dining room seats, it is $120 for the same meal. I cannot speak from experience, but I have heard the omakase experience at Sushi Yasuda is beautiful and more intimate. 

Sushi Nakazawa or 15 East Restaurant are the best go to for Omkase in NYC

Second that Sushi Nakazawa was fantastic. 

 And 15 East Restauranthas also been my favorite for years. 

A bit under the radar is New York Sushi Ko - chef worked at Masa and 15 East and trained in Japan. You can do their Sushi Mono omakase (roughly 15 pieces of fish) for about 80 dollars. Also great wine pairings. Note this place is for people who are serious about their fish and prioritize that. The chef can be known to kick out those who aren't that!