I have a '91 sport and am going to go with a 3" trailmaster lift. Should I go with 32's or 33's??

31 or 32 if you don't want to cut.....33 you will have to trim the inner fender at the rear/bottom..

So stock I can fit 30's, but if I lift it 3" I can only fit 32's. Am I missing something?

Lifting it up 3" only moves it one direction, up! The bottom of the rear fender is still next to the tire, only closer with the 33s. That is the way lifts work. Just because you lift it up 3" doesn't mean you can run 3" larger tires. Your suspension also has limits, mostly dealing with widths though. For instance my 32" equivalents rub on my swaybar at full lock. I could put a 6" lift on my Explorer (unfortunately none exist for my '97) and I still couldn't get a larger tire under it without it rubbing also without doing more mods than just the lift.