Baltra airport is in the middle of an alien desert, and if you fly in with Avianca, transportation to the boat crossing is provided (not if you fly with Tame). The trip to Puerta Ayora took 1.5 hrs and we were about to melt in the heat by then. Then we trudged around with our big backpacks looking around for boat tours and hostels for a good part of the sweltering afternoon. The tour operators roughly quoted similar prices, but we stuck with one that was marginally cheaper and included free wetsuits/snorkels.
We were on board the Millennium, which was a boat made in the stated year. Overall the furnishings were showing some wear and tear but generally pleasant. There is one room on the boat with an extra bed in place of the balcony (which we got), so we were pretty jealous of the others. Food wise, every meal was delicious and I stuffed my face 3 times a day. The crew was also a jolly bunch and took great care of us.
The trip started from Puerto Ayora, up the west coast of Isabella and around Fernandino, touched Santiago and ended up at Baltra. This took 6 days, and some passengers stayed on an extra 2 to circle Santa Cruz to end up back at Puerto Ayora. Everyday had an early start of around 6-7am, and consisted of as many land trips and snorkel sessions that you’d think were possible.
Our highlights were snorkeling into a cave and stumbling upon 5 black tipped reef sharks dozing, getting a shock at how large the giant tortoises were, and witnessing the back flipping dance of the manta rays as dolphins swam past while a whale gently misted in the distance. That last bit was all in one scene. Insane.
After we disembarked, we hopped over to San Christobal Island and made arrangements for a dive trip the next day. We did 2 dives at kicker rock and saw 100s of reef sharks and manta rays but probably a hammerhead. Get the thickest wetsuit you can and bring loads of snacks.
We splurged on the cruise/dive and totally felt the pain after seeing the number of charges on our bank statement. But the once in a lifetime experience was worth it, and given the choice we would do it all again (but draw out the money from our banks back home instead of the Equadorian banks $%#&@$#@)