Both GATE and JEST are eligible for IISER MS program in Astrophysics. Now if you consider both the examination then I would say JEST would be a better choice this is because JEST ask questions from theoretical physics more but in GATE it becomes more of a memory based or formulae based examination. So if you have clear concepts then you would easily be able to crack JEST. Also in GATE the syllabus is bigger but in JEST you need to know advanced topics well such as tensors, Abstract Algebra etc. So both are complementary to each other but if you have good concepts then JEST will be more enjoyable for you.

I hope this answer helps. All the very best for your future endeavors!