Whenever you see a truly breathtaking image, you can be sure that it's the culmination of doing a whole lot of things really, really well. In the examples you indicated, we're looking at images scaled to a size much smaller than the files produced by your camera, which suggests that at least some of the impact you're perceiving in the photos you're trying to emulate results from factors other than just sharpness and noise.

Still, a good, sharp image is an absolute prerequisite for a great finished product. You're doing a lot of things well already, including using a tripod with remote release. In addition to turning IS off, try using mirror lockup if you can. But first, swap out your 17-85 lens for your 50mm f/1.8 lens. I've used both of these lenses, as well as Canon's 15-85, and the 50 will blow the doors off all of them in terms of sharpness. No contest.

Next, you'll want to pay attention to the setting itself. As Itai indicated, you can't make up for great light, so shooting during "blue hour" will help balance the light of the buildings with a bit of ambient light, making it much easier for you to achieve the sort of exposure you're looking for. If you're shooting single shots, you might see some great results during "golden hour", as well, but if you're shooting a panorama, you should be shooting on "M", and you'll need to be aware that lighting conditions can change very, very quickly right around sunrise and sunset. This can produce some spectacular scenes, but you'll have to work quickly to make sure your panorama doesn't show lighting changes that occurred while you were shooting a set.

Itai also mentioned wind, with respect to tripod stability, but in your case, I think the biggest effect is actually on the reflections in the water. Part of the impact of the images you're emulating is that perfectly glassy reflection. Unfortunately, there's nothing you're going to be able to do, short of photoshopping in the entire skyline upside down, to produce that look if it's windy when you shoot. The good news is that the work you're doing to learn and prepare will help you nail the shot when you finally see the right conditions.