Tristanian: Although Stennis is referenced to as a 'poisoner' in a cutscene, during the end of chapter 3, it is
very clearly stated in the journal that the actual culprit, was Philippa.
Direct quote from the "Vergen Besieged" quest :
"...Among Philippa Eilhard's abandoned possessions, Gerald learned a shocking truth. It turned out it was the sorceress that poisoned the Dragonslayer ! Our hero had no idea what caused her to do so. But he guessed his finding was a trail of a bigger intrigue and saw all the previous mysteries in a new light..."
You get this entry after searching Philippa's house at the end of chapter 2, in order to shed some light into why she and Saskia departed so suddenly.
Taleroth: In this case, the journal is incorrect. There is no evidence to support that she did the poisoning, only what she did afterwards.
It may be accidentally left in from a previous version of the game where that was indeed the plot, but it's not how things are in the release version.
Or the reference in the cutscene might have been left there from a previous version, take your pick.
No evidence you say ? You find a book of poisons and antidotes in her house. Gerald himself states that such books describe both the poison and particular antidote in great detail. Philippa knew that the poison that would otherwise kill any ordinary man, would not have such a severe effect on Saskia due to her dragon origins. She knew exactly how to treat it. It was the perfect opportunity to charm her and manipulate her. She had both the motive and the tools.
On the other hand there are only circumstantial evidence against Stennis. Suspect : Thorak clearly proves that it was the priest that performed the actual poisoning deed, so to speak but it is never clearly revealed whether Stennis ordered the poisoning.
Either way there is no hard evidence against either party (eg a testimony of a witness) but in my eyes at least, Philippa had a lot more to gain and relatively little to lose when compared to Stennis. He is a lot of things but I find it hard to believe that even in his arrogance, he wouldn't realize that such an action would diminish his chances of truly being recognized as a ruler, considering that a poisoning would inevitably arouse suspicion and lead to the event as we experience them.