Unfortunately I can't comment directly on the Pioneer, but with the Sony BDP-S550, there is very little difference in the picture quality between the two from what I can see - the standalone Sony just pips the PS3, but I really had to look to notice. The main difference is in the sound, with the standalone Sony again producing better results, but much more noticeable, especially in the low end (this is running through my Onkyo 905).
Having said all that, the PS3 is certainly not a bad Blu-Ray player (still rated 4 stars by WHF compared to others around the same price) so you certainly won't be suffering a huge picture + sound quality loss with it, but there are unsurprisingly compromises when compared to the best standalone players at that price.