Presumably you mean the Canon 100mm L?
Both are excellent lenses, but your choice will be down to your main use. If you are shooting flighty insects like butterflies, dragonflies etc in the field I'd recommend the Sigma. If you are shooting general macro, including smaller bugs, flowers etc then the Canon wins.
The Canon is smaller, lighter and probably has a better IS system. Both lenses suffer a reduction in IS performance as you approach 1:1 magnification. However, the working distance is shorter than the Sigma, which can scare off insects more readily. The Sigma is heavy, but has an decent tripod mount - I use mine on a monopod rather than a tripod as it is more flexible - which makes portrait format shots easy. Can't comment on differences in sharpness, but can vouch that the Sigma is top class.