Both have their merits and demerites.
GIKI was until recent years the cream of the cream well recognized in South Asia, even today it leads in events, research, creativity, competitions, etc. which should be your top priority if you want to do masters. On the other hand, there is pressure of studies and being in middle of nowhere can make you homesick/bored very quickly although the campus is vast but sooner or later you will have explored it all.
On the other hand NUST has closely comparable facilities labs, equipment etc. A lot of the new faculty is arriving from US/UK and is equally competent however there is still some level of red tape in research, access to funding, etc. On the positive note, its a huge campus, huge social support network, better response for employment due to strong alumni network, and you live in Islamabad in peace.
At the end of the day, its your choice, your passion which must guide you and you should be realistic in understanding your own goals; do you want to work after bs or pursue ms; will you prefer to settle here or abroad; which specific sub-technology do you want to major in etc. For example, a person who wants to pursue a career in building rockets should choose a field that gets him placed abroad; a guy who likes to design dams can choose a line that keeps him in Pakistan hope you get my point.
Both places are highly competitive and simply keeping up with your classmates will make you more competitive as well. Similarly, both electrical and mechanical fields while completely different, are still highly valued as they are integral in each and every industry.
Last word: employment, jobs, further studies, integration in society is all Allah's decision not ours. The sooner you understand that the better, and why worry about whats not in your control? Focus on your passion and all the best.