Tips on applying that were originally writtend by Janice Glasgow when she was on the committee and updated by Ian Witten in 1996 can be found at http://www.cs.ubc.ca/~little/glasgow-grant.pdf
They have other sources, but many require matching funds from industry
The Canada Foundation for Innovation (CFI) (http://www.innovation.ca/index.cfm) provides funding mostly for infrastructure (e.g., large equipment, etc.)
the Networks of Centres of Excellence (NCE) (http://www.nce-rce.gc.ca/index.htm) funds partnerships between university, government and industry