Onyx is OK, in an eccentric way. I usually find unusual gemstone names kind of tacky, but there's something charming about Onyx. It has that exotic & mystical feel to it, but it does not sound like it was taken from a trashy fantasy novel.
I generally associate gemstone names with femininity (probably because most gemstone names, like flower names, are feminine), so I think I'd rather see this name on a female. But since it's so rare that it isn't heavily used by either gender, I don't see why it couldn't work on a boy as well.
Some Onyx combos, for your amusement:
Onyx
VeronicaOnyx
CassandraOnyx
DeirdreOnyx
AugustaOnyx
CordeliaOnyx
WinifredOnyx Jezabel
Onyx
SeleneOnyx
PhilippaOnyx Evening
Onyx
SalomeOnyx
IshtarOnyx
AdelheidOnyx
DorianeOnyx
WrenOnyx
IvanaOnyx
HecateOnyx
EvangelineOnyx
FelicityOnyx
DemelzaOnyx
ChristianeOnyx
HedwigOnyx
SelmaOnyx
CiaraOnyx
LucindaOnyx
SofiaOnyx
PhyllidaOnyx Edelweiss
Onyx
SophroniaOnyx
WinterOnyx
SamaraOnyx
UrsulaOnyx
Zahira Onyx
GiseleOnyx
PhaedraOnyx
FatimaOnyx
DorotheaOnyx
ZaidaOnyx
FairuzaOnyx
Junia