I work in Galapagos diving so rarely offer naturalist cruises except to liveaboard clients. Read: Not a conflict. All but Linblad mentioned above are agents, not operators. That's not always a bad thing as customer service can sometimes be better than when booking directly with Ecuador companies. English as a first language can also be helpful. If you are going to book direct, be sure they don't charge a huge processing fee on credit cards and/or do have a bank account in Miami just to make paying much easier. Folks are always a bit taken aback when asked to PayPal or transfer funds to another country.
Try to get an itinerary that goes out west: Punta Espinosa, Punta Vicente Roca, Tagus Cove, etc. The western side of Isabela is so remote, even in Galapagos, with spectacular vistas and wildlife. Isabela Island has large penguin populations, the most manta rays and is where you would most likely see whales and orcas. Flightless cormorants are not located further east. And at times, you can see 5 active volcanoes at once. Serious birders like eastern itineraries better due to being able to check off the medium tree finch on Floreana, red footed boobies, etc. Blue footed boobies, turtles, sea lions and marine iguanas are abundant and everywhere, so move on to other must sees on your list.
If you want to compare land visits, go to this link at the Galapagos National Park to get a good idea of what the visit entails:
http://www.galapagospark.org/onecolmap.php?page=sitiosdevisita_index
Ask questions before you book. The naturalist guide will make or break your visit. Class III naturalist guides are the best. Many boats will book Class I to save money. Skip them.
