Canon has some catching up to do with respect to sensor performance as measured by http://www.DxOMark.com. Canon doesn't even come close to the top performing Nikons. (High score is better.):
Canon is behind on DR and noise due to a Sony patent they apparently are having trouble working around. That said, DxO is a complete and total joke. This is a company that ranks consumer DSLRs above medium format digital backs in IQ.
Let that sink in for a moment. Their testing methodology actually results in higher scores for APS-C sensors than for MF sensors. (Queue the DxO fans claiming that their overall IQ scores don't report overall IQ, except of course when those same fans wish to prove that camera A has better overall IQ then camera B.)
I've personally tested DR for a number of cameras (the right way). My results match results from sites like DPReview. DxO is always off, and always quite obviously wrong. It's not by a set amount in each case such that you could say their test is too sensitive or not sensitive enough. It's all over the place, over in some cases and under in others. It's like the idiots never tried shooting the cameras they test.
Canon is not so far behind in sensors that I would avoid choosing them. They're behind a little bit, not a lot. But my problem with them is that they are charging more and/or skimping on features at a time when there's an IQ gap. When your competitors have a sensor edge, you pound them on features and price. The 6D should have a real AF system and be a bit cheaper. The 5D3 should be priced against the D600. And there should already be a 45 MP FF that is priced against the D800. Oh, and cut out this 20/21/22 MP nonsense. Just go to 24 MP on FF. That's not enough of a change in pixel density to affect anything. (Though I suppose they may be trying to increase wafer yields with redundant circuitry that might eat into the MP they put on FF. This may also be the reason why the 6D uses a different sensor.)
This is a recent issue with them. Throughout the 2000's they dominated sensor IQ, feature set, and price. They're also getting greedy with new lenses. Again, they're not terrible here. It's just annoying to seem them slip behind. I sincerely hope they improve in all respects because their lens library is the best out there.