Megapixels only count when shooting stills.*
What you should look at is image quality. Both cameras shoot 1920x1080 HD. Which one delivers the best images?
Which one produces less artifacts, less moire?
Which one produces a better picture at higher ISO values?
Which one dilevers a better codec?
The amount of megapixels not that important for video. The processing of those pixels is.
When shooting stills going from 17 to 20 MP isn't that much of a difference in dimensions.
A 17MP picture has a longside of 3a.
a comes from 6a^2=17MP
a = 1683. So the long side is 5049 pixels.
A 20MP picture has a long side of 3b
b comes from 6a^2=20MP
b = 1825. So the long side is 5477 pixels.
This means you'll have 420 pixels extra on the long side of the picture.
At 300dpi that adds almost 1.5 inch.
It only matters a litle bit when printing pictures above A4 at 300dpi.
So IMO megapixels shouldn't be your main reason to get the camera if you want to shoot video/movies with it.
Check out how the video files compare to each other
That depends on how the image is processed.
You can see it that way, but it is based on sensor size only.
More pixels can also mean the readout of the chip is slower, which results in more rolling shutter.
Canon DSLRs do line skip on the sensor: this creates moire and aliasing. (And the amount on lines is lower than 1080, which creates softness.
Does the Nikon process the whole image to scale it down?
If yes: changes are the image quality is better.
But you need to check that out to be sure*, otherwise you buy a camera based on a hunch.
Sharpness also depends on the lens-body combination. The Canon 1.8 50mm is a great cheap lens, but maybe not the sharpest.
* The proof is in the eating of the pudding, not in he size.
Canon's 5Ds has 50MP, but performs worse in noise/ISO and rolling shutter than 17MP models.
I need to do more research on that. Knowing Nikon, if they're not already giving Canon serious competition with DSLR cameras, they're on their way. Nikon was the professional photographer's choice for decades. They built a reputation for the best lens in the industry.
I still have a Nikon SLR with a variety of lens. Haven't used it in years now, thanks to digital.
If you use both cameras on the same shoot, you should go with what Walter is saying. I almost always shoot with two cameras as it cuts my day in half. And I did a test with a Canon 5D Mark II and a Nikon D800, and the footage looked different. It just looked like I'd have to do a lot of post production to make it look similar.
If you use only one camera in a shoot, or if you're a color grading pro, then it may not matter.