We used Aqua Expeditions for an upper Amazon River Tour (https://www.aquaexpeditions.com/cruise-ship/aria-amazon/). It was one of our most memorable trips. Great Naturalists Guides that were excellent, interesting daily tours through the rainforests and tributaries of the river and excellent cuisine on board. Very small groups so we got almost one on one attention.

For our Galapagos tour we went on a 96 passenger Celebrity ship. Which was enjoyable because they broke us down to 16 person groups. There are a number of other tour companies that use small boats with between 8,16 or 32 passengers. Choose the company with boats/ships that most fit your travel style as they all visit essentially the same parts of the same islands.