Hmm... I would say to go for dried fruit, trail mixes, etc.
Fresh organic fruits and vegetables are pretty common these days. For example
らでぃっしゅぼーや and it`s kin. We buy our vegetables through them, and they offer various gift packs if you`re just aiming to give someone something organic without it necessarily being from overseas.
As for seeds - I really can`t see why you`d want to send any? You can buy pretty much every type of seed and bulb with ease inside Japan - and any you can`t are certainly going to be against the law to import.