Undoubtedly, you should choose CSE at BITS Goa.
IIT Bhubaneswar is a new IIT that was established in the year 2008 along with five other IITs. Following this, more IITs were set up. So, it is lost among the new IITs. Whereas, BITS Goa is one among the four campuses of BITS Pilani.
The infrastructure and faculty are at par with its other campuses. Also, if we compare it with IIT Bhubaneswar or any other new IIT, BITS Goa is better in all aspects including infrastructure, faculty, labs, library, placement, alumni network, academics, technical festival, cultural festival, hostels, campus life, mess, etc.
Another point of concern for most students is the course fee. Check out the official website to get the actual figures.