What should I prefer: IT at IIIT Allahabad or CS at NIT Jalandhar?

You should without a doubt go to IIIT Allahabad for IT. When you have one of the finest institutes in the country itself, why go anywhere else? Also, you would find the same syllabus pattern which IIIT Hyderabad for CS follows. 

Keep this clear in your mind that you might not necessarily make it right away on your first try. If you look at the cut-off for the first session, it is around 5000. But if you check the previous year's cut-off, you would see it is 8000. However, you still can opt for IIIT-A, Amethi campus for your B.Tech course of 4 good years. This campus is also renowned as much as others. This would transfer you to the Allahabad campus after 4 years and it would be way better than going for CS at NIT Jalandhar in terms of grabbing company and placement opportunities. 

To give you a second option, you can consider IIIT Allahabad for the 5-year B.Tech+M.Tech which would go along with robotics, intelligent systems, info security, etc. In case you can manage a dual degree course pattern, check out B.Tech and MBA. 

With personal experience of B.Tech IT at RGIIT Amethi, I would recommend you to go for it with so much confidence.