Indian Maritime University (IMU) Chennai is obviously better than Vels University. It has a brand of its own and is known outside of Chennai as well. Vels University, on the other hand, is just like any other university and anyone hardly outside Chennai even knows about it. 

The study environment at Vels University is not at all good though other facilities are good to decent. I would say that if you want to relax and just want a degree after 3-4 years of enjoyment, go to Vels University. Otherwise, IMU Chennai is the one to go for.