Depends on the kind of person you are. I had both so I'm speaking from experience. I'm an Electrical Engineering major, so we're pretty much the same damn thing. I'm also assuming you're going to be living in the dorms.
The Desktop is a whole lot more usefull when you're playing dorm-wide lan games with tournaments between floors/buildings/dormitories. It also means more storage power for downloading/sharing/whatever. It has more power and with the bigger screen that usually comes with, easier to program because you have more space to do things. I also find that when sitting hours on end at a computer, a desktop is much more comfortable with the full-sized keyboard and such. The keypad does so much.
The laptop is great for going to the library, attaching to the many ethernet ports around campus/wireless if they have it. It was mainly a portable multimedia station for me carrying nothing but music, movies, and such. As an engineer, you won't be in the library or anywhere else to be exact. You'll be at home/parties/computer lab. As you can guess, the computer lab already has computer labs you can use.
In conclusion, get the desktop. That, or if you must, say you have a 1500 budget, spend 900 on the desktop, 600 on a decent laptop that will be able to do anything you'll need to do thats related to your major.