Hi Jayden,
I don't know about Masters but I am currently doing my BSc in Computer Science online from University of South Africa (Haven't been able to attend physical classes for years due to health reasons).
It's been really smooth. I register my units and pay online. They courier my course work and assignments. You do assignments and submit online. Then I do exams at their local centres in KCA or Inoorero.
For BSc, each unit is about Ksh. 10,000 so for two semesters a year the total comes to around 120-150k.
They have one of the best online programs and more importantly, they are accredited. The other institution I picked up when looking was University of London. For that, you sit your exams at the British Embassy. But their costs were on the higher side.
Cheers.
Wangila