Which should I choose, IISC (ME in signal processing), IITB SysCon or NITIE PGDIE?

It is best to either secure a job either at a government-run organization, PSU, or go for NITIE. You can opt for either option.

You need to obtain the best offer at the end of the day, and securing a position in the job sector might be a good decision. Apart from that, if you do not share a valuable amount of interest in the PSU, then joining NITIE Mumbai might be the best option for you. 

You will get the chance to witness several big firms visiting the campus, alongside the addition of value to your profile and simultaneous growth. In terms of the technical courses, you should definitely research more about them, as per your requirements.