Compilation from email responses (request was for low-volume vendors)
One of my very good friends (Kevin Franzino) works for Albright Technologies (www.albright1.com). They specialize in rapid and low volume parts, and as they focus on the medical industry, their quality standards are very high. Micro parts are also a big part of what they do; you'll see the" world's smallest medical silicone component" picture on their homepage.
My old firm (www.protocafe.com) could definitely help, but they are typically lower volume than what you're looking for. I don't know if you're considering production already or still prototyping. I would still get in contact though to see if they can help you out (sandra.madrigal@protocafe.com).
You can send Sandra the file along with the durometer of the material and she can work up a quote.
If you're looking for a Bay Area source, we've worked with Wickstrom Injection Molding (http://wickstrommolding.com/home.html). They are currently shooting a relatively thin wall (< 0.020") Shore 60D elastomer part for us and doing a good job. They have a lot of experience in medical, if that is relevant, and I suspect they would take on a project in that annual volume.
Catalyst http://www.catalystplasticparts.com/ can do injection-molded TPE parts, and they specialize in lower-volume, reasonbly fast tooling.