The fuel filter is REALLY EASY to get to...just look under the car right in front of the rear tire on the drivers side (or whichever side you fill it from). For the 1989 Bonneville it is the drivers side. There is a slip nut (male) on the fuel line. You should hold the filter with a large wrench and loosen the nut on the line. Be careful...the metal lines can be corroded and if you torque it wrong you can break them. While that is not hard to fix with a compression fitting, it's extra trips to the auto store. If the first nut you try is seized/not spinning on the line, try the other end. You can always twist the filter off the frozen nut if you free the other end first. Don't get it confused with the prefilter on the fuel pump itself, which does NOT need to be changed regularly (if you search this question elsewhere some people have answered with that location). I dropped my fuel tank to fix the pump and still didn't have to change that filter, so don't drop the tank unless you are having fuel delivery problems. It is a pain because you have to move the exhaust out of the way and detach a lot of other lines, and it is possible to break the rear brake line when you're putting it back in if you aren't careful. Trust me, I just did ALL of this on an '89 Bonneville this month.
The fuel Filter in 1988 Pontiac Bonneville is attached near the fuel pump. The pump is located in the gas tank. First locate the fuel pump and then you will see there a fuel filter inline between the tank and the engine. Check it out just near the gas tank. I am uploading its image which can help you to locate it.