Well if you prefer the PS3 controller, get it on PS3. Not really a huge difference between the two consoles.
This. PS3 may have better loading times and run more smoothly. Graphical fidelity will be pretty much identical.
I prefer the Xbox 360 controller (I absolutely hate the PS3 one), so I'll be getting it for the 360.
That's only because I'm used to the 360, though.
As irishboy said, really just go with whichever controller feels more natural to you.
Xbox was the first system I got that was my own. The PS2 was my older brothers, so in terms of video games, I grew up playing Xbox with my friends...It's just habit for me.
Edit: Although if you want to get DLC earliest and have the most stable game, go with the 360 version. That's the easier system to develop for, so that version is likely to be stable, and get first-access to DLC.
So factor in those two things when you choose.