It might depend on how you want to try wagyu beef.
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BLACOWS is my favorite:
If you have a chance to visit restaurants which provide fresh wagyu beef, you might have a chance to enjoy wagyu sushi! That might be an interesting experience :)
There is a standing-bar in Kachidoki (near Tsukishima) which offers uni wrapped with raw beef. The place is always crowded that you must have to arrive before the restaurant opens. I have heard that their uni wrapped with raw beef is extremely delicious.