There is not a lot of space left for Sept and Oct as it is the height of high season, but there is some...even some discounted. You need to be experienced to dive from a liveaboard.
Honestly, diving from a liveaboard vs diving from land are like going to 2 different destinations. Divers don't put Galapagos on their bucket list for the central islands. You might see the same things, but definitely nowhere near the quantities you'll see from a liveaboard. Easy to compare to other sightings... If you walk down a street in mid-town Manhattan, you'll see large numbers of people. If you walk down a street in Small Town USA you will most likely also see people. Now pretend people are hammerheads. NYC is Darwin/Wolf and the central islands are small town USA. That's the difference. Between Aug-Nov, odds of seeing whale sharks in the central islands are virtually nil. At Darwin and Wolf, it's a question of how many you'll see. Largest school of hammerheads I ever saw in the central islands was 35..and only 2 days back to back at Mosqueras when I was diving week after week month after month year after year. Largest school of hammerheads I ever saw at Darwin was too large to count or even estimate. I stopped when everyone else went after the whale shark and just hung completely surrounded by hammerheads who just swam around me...hundreds and hundreds.
How about a liveaboard combined with an extension? That is the solution to having the 'Best of Both Worlds' for many of our clients. We have developed specialized extensions (see on our website) specifically for that purpose.
If you are going to go with the Scuba Iguana itinerary, unless you have less than 30 logged dives or their other boat is full...I would highly recommend that on Jan 5, go to Daphne / Gordon Rocks instead of Beagle / Daphne. First, it's about 1.5 hours to Beagle. 2nd, Gordon Rocks is advanced diving but your best chance of hammerheads in the central islands.
If you do decide to dive the central islands in Galapagos with anyone other than Scuba Iguana, be sure to ask to see a copy of their patente. Many in Santa Cruz operate without proper permission and there have been safety problems as a result this year, including 2 deaths. There were accidents last year as well. If they don't have a patente, they are not legal dive operators. If they do have a patente, they won't mind you asking to receive a copy or they will send you a link to where they have it online.