The goodwill closest to me is mostly old/discontinued stock from stores. They do have a couple of aisles of larger toys but I have never seen a pony there. My mom and I did try to pick up a vintage Fisher Price Little People house there once and they refused to sell it because it was on "display."
I've always had the best luck with Savers/Value Village. I go to the one nearest me about once a week and I rarely leave without a pony, though granted they are usually g3s. That said, probably 80% of my g1 collection is from the thrift store and I just found Munchy and a MGR pony there within the last 3 weeks.
I also recently found a new thrift store called Thrift Town. Has anyone else heard of it? They're located in Texas, New Mexico, California and a couple of other states. They're kind of a cross between a Savers and a Goodwill. I didn't find any g1s but I came out of there with a vintage Care Bear, a vintage Care Bear book, a vintage SSC book, a vintage Mickey Mouse lunch box and a g3. I totally need to hit them up again.