In Greater Faydark, summon the amplifiers and wear them. You will now be able to see previously invisible miniscule spider webs. These look like harvestable collectibles; however, they have the words "miniscule spider web" above them rather than ?'s. They are also tabable, although the range is very small. They can vanish before harvesting them like regular harvest nodes so don't delay!.
The highest concentration of spawn points is widely scattered throughout the first orc valley of Crushbone territory. ( -825, 80, -143 ) /waypoint -825, 80, -143. Fewer, but still some are around ( -451, 19, 109 ) /waypoint -451, 19, 109. A lot of spiders wander this area along the river, and as far as the spires. There is also a small concentration of miniscule spider webs near the entrance to New Tunaria.
You can use a Gnomish Divining Rod (250 Tinkering or purchase off the broker) to track the spider webs. Track Harvestables works as well.
Be ready to spend hours searching, more so if others are looking for them as well.