Well, i have a million questions for you and they may help you decide.
Do both places offer preop bloodwork?
How does each place monitor the pet while under anesthesia?
What anesthesia do they use?
Do they place an IV before surgery?
Do they offer pain meds?
Do they do surgery on a heated surface?
Who do you trust more if something were to go wrong?
Does your humane society do line spay/neuter, fasted paced spay/neuter, or do they take their itme on every animal?
Does your regualr vet have somebody there overnight watching the pups?
Who are you more comfortable talking about your concerns with?
Will they both pull baby teeth at the time of spay?
Are vaccines required for hospitalization that you don't agree with in either place?
Are the surgeries at the humane societ done by vets who have been practicing awhile or interns that have just gotten out of vet school?
I personally would never take Ellie to the humane society or shot clinic for anything. They have their place, but it isn't something I'm interested in. Her doctor knows her well and I trust her judgment. I know she knows what she is doing and I think it's the best choice for Ellie.

Now if you can't stand your vet, I guess that's another situation entirely.