A few of my friends graduated from both the mentioned institutes and here are some insights regarding the institutes, based on their experience.

If you can afford the fee structure of Thapar university then surely go for it. Also, if you have a good rank then you must try other central government colleges of engineering in Punjab i.e NIT Jalandhar as well SLIET Longowal in district Sangrur, Punjab.

Here is a brief comparison of Punjab University and Thapar University. 

Else, if you want to take chances in the state government college then give priorities to PAU Ludhiana, GNDU Amritsar after that you can try for Punjabi University Patiala.