Which course is better for merchant navy?? BE marine engineering or BSc nautical science??

you may choose either, thats absolutely fine. if you are interested in nautical then opt for B.Sc nautical science and if you are interested in marine engineering i.e. mechanical part then opt BE Marine engineering in any case, please ensure the qualification is approved by Director General of Shipp

b.e (marine ) is best , however if you don't get it other can be a good option