Which is best, ECE at Thapar University or CSE at Jaypee Noida?

CSE at JIIT is clearly better than ECE at Thapar. You must have a minimum JEE rank of 51,000 to get CSE at JIIT Noida. 

There are no state quota, caste quota, or NRI quota at JIIT but Thapar offers a 50% quota for Punjab state students. This results in a superior quality of students at JIIT Noida than Thapar. Due to quotas and an increase in the number of seats, anyone can get admission at Thapar University.

If a student has a 300,000 rank in JEE Main, he will not be able to gain a seat anywhere, but if he is from Punjab, he may be able to secure a place in Electrical Engineering in Thapar. This explains how Thapar's situation has deteriorated.

JIIT will offer you great exposure which is actually required in CSE with regular industrial visits. CSE has more scope in terms of placements than ECE.