I've stayed at both resorts, and I enjoyed both very much. Turtle Inn is more exotic, with amazing baths and furnishings from Indonesia, but it does not have air-conditioning. (We didn't need it, as we had a seafront unit with good breezes, but should the winds go calm it would be hot.) Victoria House is more of a typical "barefoot deluxe" resort.
I think I'd make my decision on location -- whether you want to be in Placencia or on Ambergris Caye.
Oh, I see you're going in September. That's the slowest month of the year for tourism in Belize, and Placencia is particularly slow that time of year. On that basis, I'd probably lean toward San Pedro.