Crystals?

[Kirika-]

You can grow shard, but not crystals or clusters.

The best manual method of farming crystals (and clusters) is via Aetherial Reduction of DoL collectables from Ephemeral Nodes. Normally if you use cordials and +GP buffs, you can pull several hundred during a node spawn window for the given node. Just check what crystal is available for the given Ephemeral Nodes as normal slot item, the Reducible items from that node will generally reduce to the same element crystal and cluster, or use https://ffxiv.consolegameswiki.com/wiki/Ephemeral_Nodes. The nodes have a spawn timer "open" window in game of 4~6-ish EzT hours or about 12~18-ish minutes real time.
NOTE: Level 80+ Ephemeral Node Reducible Collectables produce less crystals than L60 ones, so older content is your friend for farming via this method.

The second best is using a combo of DoL skills to max the amount of shards/crystal/clusters (The Twelve's Bounty, The Giving Land, Bountiful Yield II, etc...) then hit nodes that have the elemental type you need. Due to the CD on one of the skills, plus GP regeneration timings, you do have one "big haul" off a node, followed by a few minutes of singles or small quantities. Generally, save your long CD skill, The Giving Land, for nodes that already have either a item amount buff or a number of hits buff to maximize the returns on that skill.
Also, pray to RNGesus for the highest item count procs.

Third best is, if you have plenty of Ventures, DoL retainers, and the ability to keep them in rotation of their gathering venture (sending them back out as soon as they finish the current venture), you will pull in 30 per retainer per venture every 40 minutes. The max amount of retainers currently in game is 10 per character, and if you have them as all Botany or Miner DoL jobs, you can pull 30 x 10 = 300 every 40 minutes.