You would have far more options opting for a manual gearbox with a CNG engine. Since you are used to a manual, this should be fine, and we would suggest you look at the Hyundai Exter or the Tata Punch.
Both have the dual tank CNG option, which sits below the boot floor, thus leaving you with enough boot space, and both cars offer you a slightly elevated seating position and an easy entry and exit.
If, however, you would like to opt for an automatic, an AMT – which is the only type of automatic available with CNG – will not be a very smooth gearbox as far as automatics go, but in heavy traffic conditions would still be better than a manual. In this case, look at the Tata Tiago, which also has the dual CNG tank advantage.