As mentioned, Akihabara will have plenty of stuff. If you have limited time or don’t want to walk around that much, definitely stop by the multi-floor department stores. They have a bit of everything and you can browse them relatively quickly.

You’re also likely to find some themed designs at the area Uniqlo.

If you weren’t looking for a specific anime series, you can get graphic tees practically anywhere in Japan from department stores, Shimamura, uniqlo and the like will have a selection of then.

The Akihabara area is an obvious place to visit if you’re interested in anime stuff. Many of the shops are more focused on collectibles like figures, stationery and pins but there’s bound to be an anime clothing shop in there somewhere.

Tokyo 1st street under the station has a bunch of small themed shops. Likely their clothing selections will be very small if at all but you may find some series you like.

Close to Yokohama Sakurajima station there was a Shonen Jump store if you like anime and manga from that publisher.