As with most Sea World locations, there's not much indoor seating around (if any) but there are quite a few umbrella covered tables. If you walk around the area a bit, you might find an unassuming "coffee and soft serve ice cream shop" that has fully covered open air seating (which would be to the left of the Pretzel Kitchen, when looking directly at the building).
As far as crowds go, if the place it packed… it's probably because one of the nearby shows just let out. Give it 15 minutes and the lines will be much shorter. One of the best times to visit Mama's Pretzel Kitchen is while a show is going on at the nearby Shamu Stadium!