Hi there,
Cheapest option was as James suggested to fly from Guayaquil. I would not book a cruise in advance unless you are really pushed for time. I saved $100 by not booking on the mainland and went on a boat called the Enterprise if I remember rightly (cost me $550 for 6 days). This was a boat that had something of a dodgy reputation because the owners did not get on with the travel agents. Many would not even bother telling customers about it.
The result was a pretty good trip - boat and crew were ok and the route was the same as all the others. The islands are fantastic whatever boat you take it would seem. My only criticism was the lack of attention to detail offered on the boat - the wildlife chart was for the north Atlantic! The boat was fairly big - 25 people in good size cabins. Take a good supply of alcohol and snacks though!
Can find some more specific info if you need it.
Cheers.
Matt
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