The cheapest cheese I’ve found in Tokyo has been at OK スーパー or OK Supermarket.
It doesn’t look like there are a ton of them around in Tokyo, but if one is close to you, check it out. オーケー株式会社 | ディスカウントスーパーマーケット (ok-corporation.jp)
Go there for big blocks of cheddar, gouda, and the like at discount prices. Definitely a luxury in Japan where cheese always goes at a premium and way more than I was used to back in the US.
The pizzas at OK Super are also worth giving a go, especially for the price you can get them at. We’ve had many a house party where we picked up several of their pizzas and it was a hit with all of the guests.