For crystals, the fastest way in my opinion is to farm them from nodes with BTN/MIN. Find a low population area and create a grid, then let Miqo do the rest.
For clusters, I’m not sure what’s the fastest, but Mor Dhona has unspoiled nodes every few Eorzean hours that carry clusters. I made a grid and wrote a scenario that waits for the nodes and grabs them when they come up (it alternates which cluster type to go for each node). This is pretty slow but clusters are not required by most recipes, unlike crystals, and therefore they don’t deplete as fast.