If you want REALLY affordable, three of our friends are staying at Cabo Inn Hotel. They got it for $55/night including taxes. You have to book directly through the hotel (just e-mail them). It doesn't show up as available on Hotels.com even though the hotel has availability.
http://www.caboinnhotel.com/
Here's their claim to fame: Selected by Frommer's Travel Guide as the #1 economy hotel in all of Los Cabos. 22 rooms centrally located 2 blocks from the marina.
Shockingly, they get rave reviews on TripAdvisor, too. But for $55/night, I wouldn't be expecting very much.
Here are a few others that the travel agent recommended:
Los Patios for $102/night for two queens (price includes service charge and taxes). Small hotel, not on beach, farther from town. She called it "cute" and "clean". About 5 minute drive to our villa. We might actually stay here.
http://www.hotels-cabo-san-lucas.com...FR4IUAodQgYKJA
The Bungalows: small bed and breakfast, $115-$135/night (includes gourmet breakfast). Call 1-888-424-CABO to book directly. In downtown cabo.
http://www.cabobungalows.com/
Casa Bella: 1 bedroom condos, $145-200/night. To book directly, 619-342-0093. I think this is part of a larger resort.
http://www.cabo-condo.com/