http://www.mangago.me/read-manga/kono_koi_ni_mirai_wa_nai/
Only one I know of
http://www.mangago.me/read-manga/shimanami_tasogare/
This one has a bit of everything represented by different characters, being gay, cross dressing, and being transgender
http://www.mangago.me/read-manga/paradise_kiss/
Not the main characters
Is there any manga that deals with being trans, not just cross dressing