I prefer cooling pads as it is less bulky and easier to manipulate, especially when you are using it on your lap. The external fans were a great idea when I saw them and I snagged a few different ones. Most of them didn't have solid hooks and bent easily while one actually started to magnetize my case!!! I couldn't make this up lol. I had a high end HP with all metal chasis on a laptop, and I dropped a paperclip near the vent area on the side, stuck right to the case. After process of elimination, it was the fan that did this.
The concepts between the two are different as well. The laptop cooler that sits underneath blows cool air in, which is great for adding extra cooling power. The clip on fan (or the ones that I have seen) are setup as pull, to exhaust warm air out. The laptop cooler should be more effective. On top of effectiveness, with larger diameter of a fan, they can run slower and quieter than the little noise boxes hooked on.
I hope I'm not too biased in this, but the underneath laptop cooler has way more pros than those external fans. Let me know if you have any questions!