Most shuttle operators working the Nairobi–Naivasha run pick up from hotels and hostels in Westlands, Kilimani and the CBD, usually between 6am and 8am, and the vans are booked through your accommodation or a tour desk rather than bought at a window. The journey on the A104 through Limuru and Kinungi takes roughly two to two and a half hours when traffic behaves, and the morning departure matters: leave after 9am and you meet the trucks climbing the escarpment in the heat of the day.
Matatus for Naivasha generally load from the bus stages around the city rather than from your doorstep, which means an early taxi or a ride on the matatu network to reach the stage first. If you are staying in Karen or Langata, the drive to a northern stage at dawn can eat an hour before the journey has started. For a first visit, with luggage and a lake arrival ahead of you, I would book the shuttle and treat the extra cost as buying back the morning.
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