It depends on the kinds of projects that you plan to develop. If you are pursuing theoretical Computer Science, there are NSERC, Innovation.ca, and Innocentive (although the latter can be privatized). If you plan to collaborate across several fields, you can add to the aforementioned CIHR, SADI, NCE competitions, IDRC, GenomeCanada, CEF, Canadian Space Agency, TDP, NRC, NIH, MITACS. The list continues, but the major grant competitions in academia for non-humanities/social sciences are NSERC and CIHR.
For a full list of agencies, the canada.ca website is a great resource to start you off.