I have friends pursuing courses you mentioned above at either institute. Based on the discussion I have with them, here is what should be best for you,

1. The institutes can be considered quite equivalent to one another, but BITS Goa has an upper hand. 
2. M.Sc at BITS Goa can be specialized following the first year, during which you will be allocated a B.E course depending upon your CGPA. 
3. With a 6 CGPA, you can get Mechanical Engineering, which is quite an easy job. In contrast, it is better than ICE.
4. However, if your scores are high enough then you might get a seat in CSE. 
5. By the end of 5 years, you will be receiving a B.E and an M.Sc degree, which is nonetheless a smarter choice. 

However, the fees at BITS Goa are quite a lot.