Which is better, CS at NIT Allahabad or IT at NIT Surathkal?

Honestly, there isn't any major difference between CSE and IT branches as both are related to computers. The job opportunities are almost similar. So, you should prioritize college over branch in your case. NIT Surathkal is much better than MNNIT Allahabad and this can be further understood through the points below

Location: NIT Surathkal has an advantage over NIT Allahabad due to its location near Bangalore, the IT hub of India. Most Bangalore-based companies firstly visit NITK Surathkal. Last year major companies like Microsoft, DE Shaw, Uber, Amazon, Oracle and visited the campus last year.

Coding Culture: Recently 23 students from NIT Surathkal were selected for Google Summer of Code (GSOC) which is 4th Highest in the World. It has secured 13th Rank in the ICPC Asia Contest which is the highest ranked of all NITs. NIT Surathkal is the only single NIT that became a finalist in the ACM ICPC World Contest.

Academics: Every year students win International awards proving that their academics are better than MNNIT Allahabad. 

Campus Life: The campus life of NITK Surathkal is also better than NIT Allahabad as NITK Surathkal has a private beach with a lush green campus of 300 acres and its fest Incident is the largest Cultural event in South India

Placements: Refer to the table below for comparison of placement statistics

In all, NIT Surathkal seems to be a much better option than MNNIT Allahabad after considering various factors.