i mainly know ftm mangas so if you’re alright with that here they are:

• claudine by riyoko ikeda (straight ftm mc)
• haikei, seken-sama by kanzaki shin (straight ftm mc)
• niku wo hagu by tooda oto (straight ftm mc)
• boys run the riot by keito gaku (straight ftm mc)
• after school mate by umino kuon (ftm mc)
• yuzu no koto by arai shou (ftm mc)
• f compo by hojo tsukasa (straight ftm important character in a relationship with a trans woman with non-binary/genderfluid child + has a lot of mtf side characters and one ftm side character just a warning it’s very outdated but tbf it’s from 1996)
• requiem of the rose king by kanno aya (intersex ftm mc)
• double happiness by sugiyama fumino (biography of a irl trans male lgbt activist)
• our dreams at dusk by kamatani yuuki (ftm important character + has a lot of lgbt characters)
• yuureitou by nogizaka tarou (bi ftm mc)
• sakura-chan to amane-kun by asazuki norito (straight ftm mc + crossdressing male character but tbh i read it as a closeted trans girl)
• villain by fujita & teniwoha (unlabeled/non-binary character mc x unlabeled/non-binary character mc)
• fire punch (not about transness per se but it has an important ftm mc)

haven’t read these/don’t know a lot about them but if you’re interested:

• boy meets maria by eguchi kousei (BL that deals with gender identity but read the warnings before hand)
• love me for who i am by tozaki ei (non-binary mc and if i’m not wrong it has lots of lgbt characters)
• G.I.D by shouji youko (ftm mc)
• stop!! hibaru-kun! by eguchi hisashi (mtf mc)
• echoes by ayumi (ftm mc)

transness isn’t the main theme but it has trans characters:

• dorohedoro by hayashida q (side mtf character)
• gunnm by kishiro yukito (supporting ftm character)
• level e by togashi yoshihiro (supporting ftm character)
• liar game by kaitani shinobu (side mtf character but from what i’ve heard she isn’t treated well)
• skip to loafer by takamatsu misaki (supporing mtf character)
• moriarty the patriot by takeuchi ryousuke (supporting ftm character)
• alice in borderland by aso haro (supporting mtf character)