Both colleges are best according to their respective. You can go to anyone you will learn same about ECE . But as you know NITs are ia government funded colleges and consider next after IITs but in NIT Arunachal Pradesh you might face sometime language barrier and placement and  staffs are great . But the college's is quite far so there is problem in travelling facility . There might also be some campus problem as college is quite far . But looking IIIT jabalpur it's a private college  but it also provides a great teaching and placement. Remember every college has their pros and cons but getting NIT and IIIT is achievement in yourself.