Tsunaki sushi (鮪喜)
Tsunaki is a seafood izakaya which serves really affordable and tasty dishes. Of course, they have sushi, but they also have a wide array of other Japanese dishes you can also try. If you're craving sushi, but you're with someone who doesn't like fish, let alone raw fish, you can suggest the tempura! For lunch, you can get away for under ￥1,000, and for dinner, for about ￥5,000.
Edomae Bikkuri Zushi (江戸前びっくり寿司)
As you walk out of the East exit of the JR Ebisu Station and walk about a minute, Edomae Bikkuri Zushi is quite easy to spot because of its flashy exterior. You can sit at the bar and watch the sushi chef make the dishes right before your eyes. You can order a la carte or get a set if you don't really know what to order. You'll be impressed by the price/quality ratio!
You can have lunch for under ￥2,000 and dinner for under ￥5,000.
Ebisu Yokochou Nikuzushi (恵比寿横町肉寿司)
This restaurant is tucked away in Ebisu Yokocho, which is an awesome place to grab drinks and tasty food with your friends or to meet new people. Ebisu Yokochou is an agglomeration of small bars, and among these is Nikuzushi! They specialize in meat sushi and they serve raw or broiled beef, horse and chicken. It might seem unusual, but a lot of people rave about the incredibly tender and tasty meat.
Sushi Kyoutatsu (すし京辰)
Sushi Kyoutatsu is located in the Atre building, directly connected to Ebisu Station. They serve great sushi in a modern setting. The sushi served is Edomae style sushi with red vinegar which isn't as sour. Also, getting lunch under 1,000 yen is also possible.
Lunch is under 2,000 and dinner is less than ￥5,000.
Hashiri Dokoro Sushi
This restaurant is definitely high-end and dinner is easily between ￥10,000 and ￥20,000.
However, lunch is really affordable and lets you get a taste of the refined and delicate cuisine. You can get a lunch set for ￥1,500 which includes shirashi sushi as well as other side-dishes and ice cream.