Stowe blames slavery on the owners who profiteered on human misery. In my mind, she is quite direct about this. One of the reasons why Stowe's work was so pivotal in American History was because of its direct and simple nature. In Stowe's mind, the reason for slavery resided squarely on the shoulders of those individuals who profited from it and defended it. She is quite direct about this and this is the reason why the book was so controversial at the time. She doesn't mince words on it nor does she explore the complex politicizing of the issue at the time. In her mind, slavery was immoral in its treatment of other human beings and those who engaged in it and defended it were immoral and to blame for the the condition of servitude in America of the time.
This is open to debate, as you're talking about the background motivations of an author in the 1850s. The novel itself was written in response to the passage of the Fugitive Slave Act, requiring Northerners to aid the recapture of runaway slaves. In this sense, she blames lawmakers.
On another level, Stowe blames slaveowners, some of whom are portrayed as kind and paternalistic in the novel. To her, slaveowning is an absolute moral wrong, regardless of how kind or cruel an owner is.
Lastly, I think she places blame on those in the North who tolerate slavery, or refuse to take up the abolitionist cause. I think she is most angry with this crowd, particularly northern Chrisitians.