There are many tour agencies in Puerto Ayora, ranging from competent, experienced professionals to sleazy con men on the street who would gladly sell their own mothers to a passing battleship if there was $5 in it for them. To avoid the latter, stick to places that have a real office and NEVER deal with anyone who approaches you in the street.
If you can, check the website of a place youâ€™re thinking of doing business with. If it looks serious and professional the place is probably okay. Stay away from the cheeseball hole-in-the-wall places near the old pier (close to the Proinsular supermarket).
Many of the hotels have travel desks to help their guests. If yours does, take advantage of it. These are a great way to set up little tours, buy tickets for the ferry, etc.