Armed officers used explosives to break down the door before arresting Miguna, a witness said.
"There were several blasts heard at his home before he was finally taken out," said a neighbour who did not want to be named.
Miguna is a provocative firebrand who attended the Tuesday mock swearing-in of opposition leader Raila Odinga as the "people's president", in defiance of last year's election that saw Uhuru Kenyatta win a second term.
On Thursday he goaded police, daring them to arrest him saying he had signed Odinga's oath, "So if you want to take me to court for doing my job, come baby come!"
Miguna's arrest follows that of TJ Kajwang, a lawyer and MP who was arrested on Wednesday and is due to be charged with treason and unlawful assembly.
Both men played prominent roles in the mock swearing-in, flanking Odinga as he took an oath while clutching a Bible, Miguna is his trademark kufi cap and Kajwang in a judge's robe and wig.
Their presence was particularly important given the absence of all three of Odinga's partners in the National Super Alliance (NASA) coalition.
While Miguna lost in his bid to become governor of Nairobi last year and holds no official position within NASA, he is the self-styled "general" of the party's "National Resistance Movement" wing which is tasked with implementing a threatened programme of civil disobedience and boycotts.
Today's arrest is the latest twist in the long saga of Kenya's disputed elections which saw the Supreme Court annul the result of the initial August poll and Odinga boycott the October rerun.
Odinga insists he is the real winner and therefore the legitimate president of Kenya.
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