Not sure if you still need it, but...
I've had good success with clean and comfortable rooms at the Days Inn. You're not going to get 5-star amenities, of course, but the rooms are easily the equal or better than the BW San Marcos. IIRC the BW Tradewinds has views of the ocean/Morro Rock, but I've never stayed there. If you don't mind dated (think 1970's motel) the Fireside Inn has clean, comfortable, inexpensive rooms.