M.Sc

You can get the right answer from some students who are pursuing this course. Generally, Bombay and Kanpur are the best ones since they give their students equal opportunities for placements. M.Sc in Chemistry students sit for placements with B.Tech Chemical. So, you do get a lot of options but competition is stiff. But these vary from IIT to IIT.
So, the student at this position can answer this question better.
I would advise you to do M.Sc from Delhi University as in IITs, there are no specialisation courses.
No IIT offers placement after M.Sc (chemistry) but yes if you are interested in doing Ph.D, you can choose any IIT (Mumbai, Delhi or Madras).

Here, I have mentioned some IITs accepting JAM scores and their eligibility criteria. Form. Sc. Candidate must have Bachelors degree (Geology) and any two subjects among Chemistry, Mathematics, and Biological Science Physics. Also, the candidate must have passed 12th with Math as a mandatory subject. Form. Sc. In IITB Candidate must have passed graduation with both Mathematics and Physics for two years and at least one out of these two for three years. Form. Sc. Biotechnology in IITB and IITR Candidates must have done graduation degree in any of these (Science, Agriculture, Pharmacy, Veterinary, Engineering, and Medicine) branches. Form. Sc. Chemistry in IITG, IITK, IITB, IITD, IITM, and IITR Candidate must have done a graduate degree in chemistry and also candidate must have passed 12thwith mathematics. Form. Sc. Mathematics in IITB, IITD, IITK, and IITM Candidate must have done graduation with Math as a subject for minimum two years or four semesters. Form. Sc. Physics in IITB, IITD, IITG, IITK, IITM and IITR) or Joint. Sc. /Ph.D. (Physics) in IITK Candidate must have done graduation with Physics for minimum two years/ four semesters and also must have done graduation with math for at least one year or two semesters. Form. Sc. Or Ph.D. in Geophysics at IITK Candidate must have done graduation with any two subjects from Physics, Mathematics and Geology minimum 3 years and 6 semesters. Form. Score Ph.D. (Dual Degree) in IITB Candidate must be a graduate in any one of these subjects Physics, Chemistry and Math for minimum two years and four semester.

As the acronyms suggest MCA focuses typically on the application side whereas M.Sc. Focuses on the Science / core concepts. Hence, in general, I would recommend M.Sc. Over MCA. Having said that, there are a lot of factors that one needs to consider before making such a choice as:
Curriculum: Pay attention especially to courses covering core concepts like
Data Structures and Algorithms
Theory of Automata
Operating Systems
Programming Languages
Compilers
Technologies covered: Make sure that you weigh in the coverage of technologies from the current trend like Machine Learning, Virtualization, Python, Docker, DevOps tools like terraform, ansible etc. During the course. Hand on work: The amount of hands on work like labs, projects, practical training, internships are an important aspect to consider. Institutes offering the course: Having all the above factors the same, MCA from institute X might still fare well than M.Sc. From institute Y in some cases. It is based on factors like facilities, faculty, alumni network, joining students of an institute. You need to consider all these factors for deciding between two courses towards your career progression. Some of this analysis applies for any two courses and not just MCA versus M.Sc. Good luck for choosing the right direction for your career!