I sold Malibu boats for most of the last 15 years. during which time we had several LS engines as options. Most were LS1's being sold in their GM licensed "Corvette boat" which had many corvette cues down to the tailights , drivers seat ,emblems ,etc.
the LS1 could also be optioned in their other offerings such as their direct drive ( center engine location) Response ,Sunsetter , as well as "V" drives (rear mounted 180* with 2 transmissions one to redirect power to the shaft and strut in typical inboard location underwater) VLX , Sunscape etc...
more recently they offer the supercharged LSA from the cts V and a 410 hp L96.
My experience initially with the ls1 engines from a watersports towboat angle as this is Malibus target audience was not as great as you think it would be... The LS1 as we know does not make great power at low rpm thats why we in the car hobby recommend a stall convertor as a very effective place to start modding , especially in a wakeboard boat where they are expected to pull a boat load of people along with a thousand pounds or more of ballast up onto plane directly driven - no convertor ! a traditional SBC with less power known as the Monsoon by indmar in 325/335/340/350 hp over the years would plane out much quicker than the 375 hp LS1 would.
Toyota tried to get into the boat business about 12 years ago with their "Epic" boat which had a 300 hp Lexus sourced engine in a direct drive ( simplest form of propulsion in existence) it suffered from similar issues to the ls1 smooth running great power once the boat was up top but failed miserably when trying to plane a wakeboard boat loaded with ballast we took one in trade and me and a few buddies took it out and loaded it up , everyone had to go up in the bow to plane it , it was an "epic" fail lol
We also had more LS1's have catastrophic failures than we did Monsoons even though we sold more monsoons ! I dont think this was the LS1's fault though - I blame that on the mentality of the buyer that was typically of the "status buyer" type that wasnt typically our core watersports enthusiast buyer but rather the type of knucklehead that would run WOT for 10 miles straight on the limiter. Wanted to say " look its got a Corvette engine let me show you what it can do "
The LSA is the opposite its an absolute workhorse out of the hole the SC works fabulous for that power under the curve to get a boat up on plane with a heavy load making gobs of torque by 2500 rpm
That is enough of the history lesson for you in regards to putting one in a boat the LS1's that went in Malibus looked just like the ones under the hood of a corvette - search yahoo images for Malibu boats LS1 and you can see the different installations . They were run by a standalone MEFI controller that indmar paired with the engines so yes they were factory multi port efi , coil on plug , turnkey engines!
the transmissions during those years were by ZF and Hurth so those could be sourced to bolt on an LS engine.
Where this is looking to be a long term project maybe spend some time studying salvage channels for totalled boats and maybe buy a complete boat with everything you would need to swap the entire running gear , harness , pcm , and guages ??
if not a 6.0 or 5.3 with the truck intake and a cam should make the power down low a boat will need....
with aluminum block or heads you would need to go closed cooling rather than basic raw water cooled to have it survive well in the marine environment even in fresh water , this adds expense as well as complication over a traditional SBC all iron engine
A guy I know built a real nice wooden runabout a couple years ago as a winter project , Mercruiser based SBC 300 efi , direct drive , he is a fiberglass repair guy by trade and it came out awesome , I had sold him a used inboard trailer and a motor box from a malibu he had re upholsterred during his build good luck with your build
*edit*as for what killer ls1 brought up about 02 sensors above: Indmar only went "closed loop" in the last couple years having to add o2 sensors when mandated to install catalytic convertors on boats previous to that the controllers were pretty simple and ran in open loop with no feedback being provided by o2 sensors since therewere none - Alpha N tuning as I recall from my tuning books