Rare particles are entirely random, you can get them anywhere. Though you have to succeed at the waveform minigame and ideally complete them with time to spare for a better chance for a rare.
look at what Tier the item is you want to craft.
Tier 1 samples are found in Delta Volanis, Arucanis Arm and Hromi Cluster
Tier 2 in the Romulan clusters/nebulas.
Tier 3 in the Bajoran nebulas
Tier 4 in B'Tran for Rear Admirals
Tier 5 in VA B'Tran
The Delta Flyer schematic you get for completing the Delta Flyer mission daily ten times. means you have to pick up the mission each day and use a shuttle to collect the specific anomalies.
or if you have some resources buy the schematic on the exchange.
To craft the actual flyer you need 180 crafting skill points which you get by crafting other stuff.