Heath, Rowan, Reed, Orris, Basil...not necessarily 'flowery' but I guess would do at a stretch.

I would pronounce Ione as "Ee-Yona" so no I don't think that's so suited for a boy.

Hmmm gemstones - what about "Gem"? I knew a boy called Jade but that was about 25 years ago, before it became popular for girls.