The reptile, measuring more than four metres long, was reported to authorities after launching itself at the houseboat, and in a separate incident, taking a dog.
The animal was captured at Cardwell Marina, north of Townsville, on Monday, less than a week after a three metre crocodile was caught in the same location.
Wildlife officer Ella Meeve said due to the size of the latest animal caught, it is considered an 'icon crocodile'.
"This means the decision on where the crocodile will be placed and housed must be made in consultation with the relevant Traditional Owners," she said.
"It also means that the animal may only be placed with a registered crocodile farm or zoo which agrees to use it for educational purposes about crocodile conservation and their ecology."
Ms Meeves said the crocodiles were likely attracted to the area because they had found food in the marina.
"I am asking everyone who uses the marina to make sensible choices around the water, and that includes the proper disposal of unwanted bait and fish frames," she said.
"We believe the animals entered the marina because they could smell baited crab pots, or were being deliberately or inadvertently fed by people discarding fish frames in the area."
The crocodile has been temporarily relocated in a Department of Environment, Science and Innovation holding facility while Traditional Owners are consulted about the animal's future.
Both the captured crocodiles are expected to be placed in a farm or a zoo.
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