Yes, it is very good if in class 9th, you are above average in Physics (actual syllabus of NEET), and below average in chemistry. It is okay to be below average. Because you have enough time to prepare for chemistry. But you need to revise the syllabus at regular interval so that you don't forget anything related to syllabus.

Normally, students start their preparation for NEET after their 10th but its good if you are preparing from 9th itself.

Hope it helps.