Hi Ankur,

Honestly it won't affect your chance of getting any college in NEET PG depending upon your NEET UG choice. 

If you are getting a better college through state counselling then go for it. If you are getting a better college through AIQ counselling then for for that. In any case you should opt for the best choice. 

Counselling for NEET UG and NEET PG are totally independent counselling processes because for both you have to first sit and qualify NEET UG and NEET PG respectively 

No matter through which counselling process you get admission into a college, for NEET PG, if you qualify then again you will have the option to sit for both AIQ counselling as we as your state counselling.

I hope it helps

All the best!