Hi Namita !!!
Before talking about the best option between PAU & Thapar University, I hope that you have researched well about the various career options open for you after completing degree in MSc Chemistry. If not, I would want to brief you about some of those options.
a) Teaching is a good option after getting postgraduate degree in basic sciences like chemistry. Private institutes preparing students for IIT/MBBS entrances hire students with PG degree at starting salary of Rs 15000- 25000.
b) There are lots of colleges who are offering jobs to fresh graduates (if you clear net it will be added advantage)
c) Govt jobs are also there but that needs extra degree of B.Ed.
2) Pharmaceutical companies are also a option if you are good in analysis and have a good practical hand.
3) Defence Research and Development Organisation (DRDO) also hires MSc chemistry for different positions. So you keep yourself updated on that front.
4) Paint industry is another domain which offers opportunities for you.
5) Research: If you are interested in research you have two options.
a) Firstly, you can prepare for NET-JRF and apply for different IIT and many other good institutions like IISERS,IITs,CSIR labs.
b) You can appear for GRE and apply for different universities in abroad.
NOW coming to your question which one is better:- PAU or Thapar??
PAU is government institution and has a well established Department of Chemistry since 1965 . I think you will get more exposure in terms of faculty and research. One important point for consideration (may or may not be in your case) is that fees structure will be more reasonable in this institution. You can research and talk to the students of the institution for more information.
Follow the link:- http://web.pau.edu/cobsh/index.php?_act=manageDepartments&DO=viewDepartment&intLinkID=3
On the other hand in Thapar university, I could not find any department for chemistry.