There seem to be millions and millions of places to get CDs made online.

Which are the 3-5 best CD duplication houses for this project, and
what do they charge?

I need quotes from 3-5 different CD duplication houses capable of
delivering 10,000 audio CDs at a time.  They must:

1. Do 2-color or 3-color printing on the CD face.
2. Provide a sleeve, jewel case or other storage method for the CDs.
3. Bundle the CDs into groups in some way so that it's convenient to
give to customers.  Example-bundle together 3 CDs for program A and 4
different CDs for program B with a simple rubber band, 3-CD jewel
cases, or 4-CD jewel cases.
4. Deliver large quantities of CDs to different locations in the US.
5. Proof that they do outstanding work, deliver on time, and provide
very good customer support (probably in the form of a guarantee or
quality referrals.)

I plan on ordering 10,000+ CDs every month for many years, so I
therefore expect a price of under $1.  Right now I'm looking to try
out several vendors to find the one that delivers the best price,
on-time delivery, and service for my company.

My suggestion would be to simply try out 5 of them your first year. 

Split up the work into 2,000 CD * 5 different suppliers = 10,000 and
see which ones do the best job for you. Why put all your eggs in one
basket? You might fine that one chares a few cents more but their
service and final product are well worth it.