Stories where yakuza or thugs fall in love can be any genre.

http://www.mangago.zone/read-manga/when_the_yakuza_falls_inlove/
http://www.mangago.zone/read-manga/cover_up/

Maybe you can find something from this list of BL yakuzas http://www.mangago.zone/home/mangalist/787423/

http://www.mangago.zone/read-manga/raise_wa_tanin_ga_ii/
seriously love this one but its yet to progress to love