I can of course only speak for myself, but I found PQ3 to be far better, especially storyline-wise. Could also be that I played it when it first was released , so I didn't feel like the graphics/gameplay in general was below the average standard. I didn't get to play PQ4 until much later, but I missed Sonny Bonds too much to really get into it I guess.
This was also during a time where internet was non-excistant so cheats and walkthroughs wasn't just an alt-tabbed google-search away either so I remember especially when I (revealing spoilers in tags)
Spoiler: figured out the map-grid, drew the pentagram and found the crackhouse. God, I was SO thrilled when I first walked through that door. I must have replayed that part over and over and over again