I am a GRE aspirant, currently pursuing engineering (3rd year). How good should I score to get into the top best 50 universities ?

The grad schools doesn't generally take your school performance into account. As for your concern about your ug performance, they look at your rank in the batch. In some universities the topper scores as low as 75%. This doesn't mean that they don't get into big universities. I would say if you are in the top 15% of your batch you can get into a good college. Follow the link : Best 50 University