The preference is always given to BITS Goa as it belongs to the most reputed family of BITS institute. One of my friends has studied there and he loves the campus from all aspects.
The major reasons as to why BITS Goa is to be preferred are:
Scope
Faculty
Campus
BITS Goa makes it a better option on all fronts whether its faculty, campus, or scope. Having this outlook will help you get to a good institute. The stream can be a point of interest but other factors also matter.