You may check Birla Institute of Technology, Mesra, Ranchi Noida and Jaipur campuses. They have B.Sc in Animation and Multimedia and Masters M.Sc. in Animation and Multimedia. BIT is known worldwide for technical education. It is one of reputed engineering institute of the country and its a philanthropic institute as well.  Check www.BITMesra.ac.in for details

Hello Nayantara!
Before opting for any of the subjects, you must understand the purpose behind the study of both the subjects. The process of analysis, like the similarities and the differences between the two subjects and then recognizing the branch of engineering that would take you closer to your field of interest etc.would definitely help you in selecting the appropriate branch. Let's begin by analysing both the branches individually-
Computer Science Engineering- This branch of engineering is quite broad and mostly aims at the study of theoretical as well as application part of computer science as a subject. The curriculum of this branch of engineering includes hardware training and hardware-software interactions. Relating this to your field of interest, i.e. animation, so definitely (most probably) computer science engineering includes 'Graphics and Visualization' in it's curriculum which in some way, would bring you closer to your field of interest.
Software Engineering- Let's refer to this branch as Software Development (the two terms are not synonymous though). As the name suggests, it mostly deals with the softwares, their designing and development and may be considered as a part of computer science engineering. It mostly deals with the study of practical aspects. The curriculum of this branch doesn't include hardware development, but definitely includes the the study of hardware-software interactions. Relating this to your field of interest, so as per as what I understand, topics like 'Graphics and Visualization' aren't included in it's curriculum; but after pursuing B. Tech or B.E. in this brach, you will definitely be able to develop applications for animation and designing.
Points to be noted:

• A computer science engineer can become a software developer but vice versa isn't possible.
• You ought to understand that becoming a graphic designer (i.e. into animation) and developing applications for graphic designing (animation) are two different things.

Now I am assuming that you have enough idea about the scope of the two branches in the field of animation. Make sure that you choose your branch wisely, because that will eventually affect your career in future.
All the best! Do well! :)