When looking at lenses, it's usually best to compare one specific lens to another...because each manufacturer will have many good lenses and several not-so-good lenses. Besides Canon & Nikon, I'll include other companies like Sigma, Tamron, Tokina in that.
But you're right in that it's a good idea to look at the whole line of lenses, before choosing a brand to invest in.
I think that looking at the big picture, Canon & Nikon are not much different. Yes, there will be many differences, but overall, a good photographer should be able to work very well with either system.
Off the top of my head, I think that Nikon has been more expensive, especially with their high end lenses. But recently, Canon has been raising the price of their top end lenses, or at least coming out with upgraded versions at prices that are much higher than the older versions.
I think that some photographers will say that Canon has a better line up of top quality prime lenses (24mm F1.4 L, 35mm F1.4 L etc.) but I'd guess that Nikon primes are pretty good as well.
If you have a specific need or type of shooting that you will be doing...then you might bias your decision toward the company that has the best option for that specific need.