First off are you sure you are in manual video mode?
Go to video mode and press the menu button, one of the first two menus will have your two choices: Exposure AUTO or MANUAL. Select MANUAL.
Then select resolution and frame rate.
Back in video mode, set shutter to 1/60th (1/50th if in PAL region).
Set aperture for desired "Depth Of Field" (Zone Of Acceptable Sharpness) effect. Wide aperture for shallow zone, small for deep zone, or medium aperture for something in between. But night scenes may dictate wide for enough exposure.
ISO should still be at AUTO for the moment, press the shutter button lightly to cause settings to all display on the bottom of the LCD (you need to have the display set for this), take note of the ISO the camera will select and "dial this value in" manually. Exposure is now "locked" until you change it, the camera will not be changing it on you as you pan around.
You can, at this point, adjust ISO up or down for specific exposure effect desired.
NOISE: Check your monitor settings (from the controls on the monitor). Especially sharpening, even the very slightest degree of oversharpening on the monitor will create the effect of noise where there may be NONE. I was "plagued" with bad noise on one workstation to the point almost every video showed noise. Until I thought to check monitor configuration and found sharpening, contrast, and brightness all way too high. Sharpening and contrast were almost to MAX and brightness was up to 75%.
Pulling everything down to midpoint and then "tweaking" to taste solved the problem.
On my 7D, night tests I ran at f4 showed ISO 1600 to be totally clean, 3200 maybe a bit of noise but still looked very good, 6400 some noise showing but quite usable, 12,800 fair amount of noise except where I was able to get proper exposure in the scene (sidewalk scenes where store windows "bathed" most of the area with enough light to get good exposure on most surfaces). I would use 12,800 if necessary to get the scene and not obsess about it.