Well, I haven't eaten at San Angel Inn, but I can tell you that Tony's only redeeming quality is its location. The food was not great and the service was just okay.
Honestly, two of the worst TS for me. Tony's is overpriced, bad Italian food. San Angel Inn is a beautiful location with way too many tables crammed in, overworked servers, and not great food. We gave it a try this November after a couple of years, and were not pleased. We usually enjoy all of our meals at Disney, but not at these two places.
I have never eaten at Tony's but if I had to choose one of those two, it would be Tony's. We gave San Angel's another try this summer and we regretted it. It was horrible. Everything from the service to the food. I was so disappointed. You may want to go with a completely different choice.