The elite agency, which investigates terror cases, said these separatists - all key members of the Hurriyat and one of who is the son-in-law of Hurriyat hardliner Syed Ali Shah Geelani - were in touch with stone-pelters, about 60 of who have been identified.
Investigators have tracked their communication to locations where protests erupted with crowds throwing stones at security personnel, often to disrupt operations against terrorists, the NIA said, as it produced the seven in court.
While Bitta Karate or Farooq Ahmed Dar, a former militant accused of several killings but let off by court because of lack of evidence, was arrested from Delhi, the others were arrested in Srinagar on Monday and were brought to the national capital. They include Geelani's son-in-law Altaf Ahmed Shah, three key aides Ayaz Akbar, Mehrajuddin Kalwal and Bashir Ahmad Bhat and Nayeem Khan and Shahid-ul-Islam, a close associate of Mirwaiz Umar Farooq, seen as a moderate among separatists.
"Evidence collected so far clearly proves a financial trail as well as a direct link between terror activities and funding from Pakistan-based terror groups," NIA spokesman Alok Mittal had said on Monday.
The NIA has said it has scrutinised a number of documents seized during raids last month and will now confront the separatists with the evidence, which includes the transfer of money into their bank accounts and through hawala transfers.
The arrests were made after a two-month-long investigation and several rounds of questioning in Srinagar and Delhi. Geelani's son-in-law was interrogated for two weeks.
India has, for years, accused Pakistan of funding, arming and training Kashmiri separatists but this is the first time that so many senior members of the Hurriyat Conference have been arrested on charges of receiving money from Pakistan.
The NIA first information report names as an accused Pakistan-based terrorist Hafiz Saeed, who heads the Jamaat-ud-Dawah, a front for the Lashkar-e-Taiba (LeT), and also the Hurriyat Conference and terror outfit Hizbul Mujahideen.