I believe it would depend on the quality of the class. Even arts like Karate and Tae Kwon Do can prove to make for good classes if the quality of instruction is there. I would say to check out both the San Soo and the MT class and go with whichever you feel you would get the most from.
Consider your reasons for taking the class. Are you taking the class because you want to get a dose of "the TMA Experience?" (i.e. cultural aspects, weapons, forms, etc.) I don't know how much or in what way those aspects apply to San Soo, but Chinese styles usually offer heaping helpings of that (I hear San Soo is pretty progressive as CMA goes.)
On the other hand, if you really want to learn for self-defense purposes or because you've got a hankering to fight competitively, I would lean toward the Muay Thai class. Not because I feel that San Soo would have any less to offer as far as fighting goes, but because Muay Thai would give you a good array of basics you can train in and gain proficiency in more quickly. Plus if you want to fight competitively you wouldn't have to worry about "temporarily dropping" groin kicks and other illegal blows from your training like you would in San Soo.
Hope that helps!
"Prepare your mind..." "For a mind explosion!"
-The Human Giant, Illusionators