All of the missions had extensive livestock herds. San Juan Capistrano had large numbers of cattle (ranging between 10,000 - 14,000 head during their peak years of 1806-1827) and an average of about 12,000 sheep during the same years. Their annual reports show some goats (203 in 1820), pigs (195 in the same year) and of courses horses (about 140 on average), which we used for transportation. While San Juan Capistrano didn't have the largest herds of livestock in the mission chain, it was in the upper half.
Incidentally, not all of the livestock were kept at the mission. They maintained "ranchos" throughout the mission territory. The ones that are well documented are Agua Caliente, de los Coytes, Cienga de las Ranos, de las Flores, del Refugio, de Santa Margarita, des San Mateo and Tia Juana.