If you are efficient and hard-working, then NIT Surathkal can be the best choice for you. If not, then you can go for BITS Goa.
Depending upon various factors, the IT department of NIT Surathkal is slightly better. It is so because it is one of the most reputed NITs in the country, and IT is several steps ahead of ECE.
If BITS Pilan would have been your other option, the thoughts would have turned around. But since it is BITS Goa, then your choice must remain NIT Surathkal.