Tree of dreaming serves as the main source of runestone. This building is available only on the Island of the Ancients after completing the relevant set of quests. To construct Tree of dreaming, you should have reached level 36. Runestone requires stone and cut stone to start the production.
You can also find runestone at your friends' villages or buy it from the store at any moment. Moreover, with gems you can get another building that produces runestone: Ancestral altar. Unlike Tree of dreaming, this building is available on all islands except for Farmer's bay and Fisherman's cove.