good question. There's a lot more good trans manga than good trans anime, but we haven't watched or read a whole lot of either. Compounding the difficulty in answering this is that many of the good trans rep we have seen is in manga and/or anime that, while it might have good trans representation, we wouldn't necessarily recommend for other reasons. Or maybe we don't feel like the trans representation is of high enough quality to put on a pedestal, because it's of an ambiguous nature, for example it's commonly accepted headcanon or only paratext (meaning said by the creators but not actually enscribed into the story proper), and also a lot of names are escaping us right now because gosh wow grief.

Also, we actually don't really watch anime "for the representation"? like, we'll try an anime out if we're told it is a good story with a trans character, but a fair number of shows that have good queer representation also happen to not be to our tastes, and unfortunately the number of anime we like that don't have explicit trans/queer representation far outnumber those that do. This isn't because we don't want good representation, it's just a statistical inevitability given that explicit queer representation is far from widespread.

also youtube being bad and us watching anime for youtube sort of disincentivizes us from seeking out anime on the basis of its trans representation for the sake of making a video about it that wouldn't get much views... whoosh whoosh algorithm blah...

We're told that Wandering Son is good but haven't gotten around to it. We've been meaning to watch Fabiniku. Kashimashi has a good example of a trans character, but is not a good anime. Our Dreams At Dusk is something we're meaning to get around to. Wonder Egg Priority has trans characters in it who are handled alright, but that show is not recommended to most people. Zombieland Saga has a trans character who is good, people like her, but also not everyone likes that show for other reasons. (although they're wrong. it's good. but sure not to everyone's tastes) We need to finish Bishounen Tanteidan. Whispered Words has an egg vibes crossdressing character but we didn't finish watching that.

yeah, all of these come with some caveat or another, either because we didn't get around to or finish the media in question, or because we can't recommend the media in question for other reasons, and this is just embarrassing that we have no straight answer to this, gosh...

the real answer to this question is just bookmark dynasty reader? and read whatever of the good, bad, bizarre obscure queer manga that pop up there which happen to interest you. cause some of them have trans characters in them! and some of them might be doujins about your favorite anime characters maybe being trans, sometimes. uh yeah. also just like, be gay and vibe with whatever anime you like, regardless of if it's explicitly queer or not. you don't need anime's permission to be trans or gay.