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My understanding (which may be wrong) is that evidence would be ruled inadmissable if it was discovered in a way that compromised the 4th amendment- but they won't convict him on the evidence found in the boat, they'll convict him on the evidence in his apartment etc.

The coppers had nothing to lose in terms of securing the prosecution in raiding peoples houses- they'd just lose the ability to prosecute the home-owner if they found (for example) a forest of Marijuana plants in the living room whilst looking for the bomber.

But the bombers conviction was nailed on before they started raiding peoples houses.

The probable cause for searching people's homes for a fugitive suspect will have legal precedent, I would need to search for the specifics.There would need to be no probable cause for searching the boat - the owner called it in and cooperated with authorities in that instance.

That will be separate for the probable cause for searching the suspect's property for evidence linking him to any crime.