Well, I gotta tell you, holy crap there are a lot of places out there. Minimum order for all the ones I've seen are 500 units. Science, this is confusing. I did find a place that is actually local to me and when the orders are "too big" to be handled in their local factory get handled in China. It seems nearly everyone does their manufacturing in China if you go by the "obvious" route of googling for custom plushie manufacturing.
That's probably the wrong way of researching this. The right way would theoretically involve contacting manufacturers directly. I'm a little vague on how to go about doing that. Hopefully tomorrow's research will work out better.