We did a small ship trip there last year (Lindblad/NatGeo) and it was the best trip we ever had!
You should be fine no matter who you go with because the Ecuadorian government is extremely strict about tourism. Very small groups allowed on shore, only at specific places and times that are prearranged for minimum disruption to the animals. Very low naturalist to tourist ratio as well.
You can see from my avatar that I'm still basking in the glow of that trip.