Officers found 30 people aboard the vessel, near Hackney Marshes, at 4.30am on Saturday morning after reports of loud music.
The arrested man, aged 31, was previously reported for organising a similar gathering less than two weeks ago, the Metropolitan Police said.
Chief Inspector Pete Shaw said: “It is incredibly disappointing that incidents of this nature continue when the vast majority of Londoners are doing the right thing and making huge sacrifices to stop the virus spreading.
"Each breach of the regulations not only presents a risk to the groups congregating but also to the officers who have to deal with it.
"To have an individual who has repeatedly ignored these regulations and who appears to have organised multiple events is dangerous and indicates a complete disregard for the safety of all involved."
The 26 who were fined were each hit with a fixed penalty notice of £800, Ch Insp Shaw added.
It came just two days after police were forced to shut down another party across the city in Wandsworth.
Officers dispersed 40 people from a house just before midnight on Thursday with one woman arrested and others fined.
Inspector Matt Ebbs said: “These individuals acted selfishly and risked spreading the virus which has already claimed countless lives across our city."
Figures from ACRO Criminal Records Office show police in England issued 196 of the maximum £10,000 lockdown fines to organisers of gatherings of more than 30 people – including raves, parties and protests – between August and December last year.