Having worked at both, my sister shared her experience at CSIR IHBT and IIT Roorkee. So, I feel I will do justice to this question.

CSIR labs are national R&D organizations whereas IITs are premiere engineering institutes of higher education. 

The main focus in the CSIR lab is put on the chemistry of natural products and is well-known for its excellent biotechnology research. IIT Roorkee, on the other hand, is mainly an engineering institute with research facilities. The Institute certainly has a great research culture but like CSIR, research isn’t the primary focus, education is.

My suggestion will be to go for IIT Roorkee if your research inclination is towards chemical engineering, instrumentation engineering, or some other field. But if you want to conduct extensive research on Organic Chemistry or Biotechnology then CSIR-IHBT is a better place.