I see 3 factory proms for 1989 TPI-T5 cars.
APYS
ANYY
ANYX

Does anyone know what the differences are ?

 

Where did you get those codes from?
This list
http://www.chevythunder.com/prom_bcc_1989.htm
has
ANYX is listed as a 305 auto
no ANYY but a APYY also a auto prom

Every-time GM made an changes for whatever reason they issued a new prom ID so the differences may be minor

 

That chart is not accurate.
My oem prom is ANYX, and I have the 3:45 gears. And the scan ID on that chart is not accurate either.
But it's still good to see all the different variations.

 

There was never a "official" prom listing given out by GM so any lists published are subjective , based on what info the poster had.

 

The anyx scan is 9401 gm part number 16133630 nit all the information on caldata, bcc find or the old moates xls is correct.

 

Usually the biggest differences between the different broadcast codes will be what rearend gear ratio, and whether the chip is setup for 49-state Federal emissions standards, or California specific emissions. Those PROM's should be listed here on the site in the FAQ section in the article about factory PROM codes. If you're not in CA, I'd recommend using one with the 49-state, Federal emissions, and whichever gear ratio is the closest match to your car. You'll probably want to check both the Pontiac broadcast codes and the Chevrolet broadcast codes since I'm not sure which ones you posted apply to.