CUSAT and JNTU Hyderabad, both the colleges are good. I have few friends at both, so I can give you some insight into them.
JNTU Hyderabad is a reputed institute. According to the placement report which is given by the college companies like TCS, Wipro, cognizant, etc visits the campus.
CUSAT is a better choice than JNTU Hyderabad. As in CUSAT, you would get a lot of exposure. The facilities are up to the mark even though it is not much of a luxurious college.
You will get a proper atmosphere to learn and as far as the study is concerned you will get adequate material here for study purposes. The library facilities are good and it is quite large. You will also get adequate facilities for games and sports.
The campus placement of CUSAT also holds a better record than that of JNTU Hyderabad. For better placement, you have to work hard and pass the exams. As the syllabus and whole curriculum are a bit tougher than that of JNTU Hyderabad. Also, the ranking of CUSAT is higher than that of JNTU Hyderabad.