Can someone recommend any especially good resources (books, mags,
websites) that discuss non-pharmaceutical companies (e.g.,
automakers, semiconductor companies, other manufacturers) that are
investing in biotechnologies? I need to create a list of non-pharma
companies that are either doing R&D in-house to commercialize
bio-based products or are investing in/partnering with biotech
start-ups.

Have you spent time yet with the BIO website (trade organization)?
See http://www.bio.org/speeches/pubs/er/ for a hyperlinked overview of
the various industries concerned with biotech, including: agriculture,
food, environmental/industrial, and homeland security.
The BIO member list should include some non-therapeutic companies
investing in biotech R&D.