The hotel restaurants.
Cafe Orleans has some seats inside (I've never been seated inside though). Riverbelle Terrace has some. Hungry Bear has covered, though not really "indoors", seating. Plaza Inn has some. Pizza Port is indoors. Blue Bayou is all indoors. Golden Horseshoe is inside, Rancho del Zocalo has some covered seating but not indoors, and most of it is not really *covered* but shaded. If Enchanted Cottage still exists, it is (was?) inside the PFF area, and therefore could be considered indoors.
I think I've seen some cover at Award Weiners, but I'm not sure, I haven't been in to see the seating I've seen.
Ariel's Grotto has indoors, Cove Bar has covered seating. If Pizza Oom Mow Mow still exists, it has indoor seating. Taste Pilots Grill is indoors, and there are seats inside for Wine Country Trattoria. (don't know if the Vineyard Room still exists, and even if it does, I don't know the status of its seating, but I didn't want to leave it off entirely and have you assume that meant it was only outdoors, when I just don't know)