There are plenty of free or cheap activities to do around Puerto Ayora. What we've decided was to explore the part called "las Grietas" and la playa de las Alemanes.
To go to these two locations, you will have to take a water-taxi which costs 80 cents, which will drop you on the other side of the cliff along the harbor. Once there you will have to walk along a path towards the beach.
The beach itself is pretty small and quiet. It is a creek where you can see mangroves and iguanas. I wouldn't recommend to snorkel there as there is not much to see and the water is not clear. However, if you'd like to experience surfing in the Galapagos, it is the place to go to.
Across the beach, the path continues into the bushes and volcanic rocks. It will lead you to Las Grietas: a rift caused by an earthquake, filled up by clear water, where you can now swim and snorkel. The entrance is free, but as well as Darwin's station you will have to sign up. Las Grietas is part of the preserved area you can access for free on the archipelago.
To try to avoid the crowd I would recommend you to go there in the morning or early afternoon, as the locals are coming around 4pm. Sometimes even schools are coming and it is not quiet as you would like it to be.