Cruz del Sur is near Ormeņo and Tepsa. These 3 bus companies are located in La Victoria, not the nicest district that's right, but fortunately that is not the worst part of La Victoria (you cross Javier Prado and you are in San Isidrio). Anyway those are streets where you must take care, but they are not so dangerous. It also depends on the time you are. Late nights are not recommendable to walk around.

And yes, there is a bus company in San Isidro, it's Oltursa (Av. Aramburu), a good company too as Cruz del Sur and Ormeņo are.