ENI stands for Electronics & Instrumentation Engineering while EEE is Electrical & Electronics Engineering. Having known some people studying at both these institutions, I can say that BITS Goa is better than NIT Surathkal.

• In terms of infrastructure, BITS Goa is obviously better than NIT Surathkal. 
• Better companies visit BITS Goa campus than NIT Surathkal. 
• The course curriculum and the quality of academic projects are also better at BITS Goa. 
• The faculty at BITS Goa is also top-notch.
• In between the two branches, both are almost the same barring a few subjects (3 subjects to be precise). 
• The course load, placements, and projects all are similar between the two. 
• As these are core branches, getting placed in the core companies is going to be difficult at either of the institutes. 

Finally, I would say that ENI at BITS Goa is very good and actually might be a little better than EEE at NIT Surathkal.