Well in the original Japanese, Chrona is given neither male nor female pronouns and is never referred to as one or the other. In the english version chrona is refereed to as a boy and has male pronouns. It honestly doesn't matter whether he is a girl or a boy (I refer to chrona as a boy just because I read the english version) and it could go either way.
Arguments for female: Chrona, name ends in "a" sound which in many cultures is a feminine suffix. Wears dress/skirt. Slender body. weapon seems to be male and usually weapons are the opposite gender of their meister
Arguments for male: No indications of having a chest of any kind. English version male pronouns.
I suppose I prefer to see Chrona as a feminine boy.