Cuenca is the best-preserved colonial city in Ecuador and the weakest town in this sweep for bookable activities, which is a mismatch worth explaining. The three best-known agencies in the historic centre are all properly registered and have been trading for years; their websites are variously behind Cloudflare, JavaScript-only, or unfinished.
So the list below is short. The city rewards walking and the agencies are easy to find on Gran Colombia and Hermano Miguel once you are there.