Technically, no boats are owned by foreigners/foreign countries. All ships fly under the flag of Ecuador. However, a lot of ships are owned/operated by mainland (Quito/Guayaquil) companies. At least this is how I read it when doing research a while ago.
Our ship (Xpedition, the largest and most "foreign" in the Galapagos) had a local artist selling his canvas prints on board the last day. They had Galapagos Jewelery on board as well, but I don't know if that's truly "local". The on-board gift shop had very few souvenirs. It was mostly expedition wear/gear and sundries.
If you want to help the locals, Lindblad helps run a store called "Reflections" on the main drag of Puerto Ayora. It is all locally produced and sustainable items. And quality/dignified stuff at that. It's part of an attempt to shift some locals away from (illegal) fishing.