Altaf Ahmed Shah, popularly known as Altaf Fantoosh, was in the custody of the Jammu and Kashmir Police, who had put him in preventive detention immediately after the festival of Eid earlier this month.
Mr Geelani's close aides Tehreek-e-Hurriyat spokesman Ayaz Akbar and Peer Saifullah were arrested by the NIA from the Valley, officials engaged in the operation said.
The NIA also arrested Shahid-ul-Islam, spokesman of the moderate Hurriyat Conference led by Mirwaiz Umer Farooq, they said.
The others arrested are Mehrajuddin Kalwal and Nayeem Khan (of the Hurriyat's Geelani faction) and Farooq Ahmed Dar alias 'Bitta Karate', they said.
The houses of those arrested had been raided by NIA sleuths last month. Mr Shah is perceived as an influential force in the Tehrek-
Hafeez Saeed, the Pakistan-based chief of the Jamaat-ul Dawah, the front of the banned Lashker-e-Taiba (LeT), has been named in the FIR as an accused besides organisations such as the Hurriyat Conference (factions led by Geelani and Mirwaiz Farooq), Hizbul Mujahideen (HM) and Dukhtaran-e-Milat.
The NIA had recovered account books, Rs 2 crore in cash and letterheads of banned terror groups, including of the LeT and HM, from the raids.
The NIA investigation also seeks to identify the chain of players behind the financing of terrorist activities, including those who masterminded the throwing of stones at security forces, burnt down schools and damaged government establishments.
For the the first time since the rise of terrorism in Kashmir in the early 1990s, a central probe agency had carried out raids in connection with the funding of separatists.
In 2002, the Income Tax department had raided the establishments of some separatist leaders, including Mr Geelani, and seized cash and documents.