Here's my pick "closer" to Bellville:
Magson Marine - Strand: I'm not sure about the quality of service, as I haven't taken my motors there, but they have been Yamaha agents for as long as I can remember, and they have been around a very ong time.
Aquamall - S/West, Strand : but they are Mariner agents. I have had services there in the past with no complaints, but they were mariner motors. I would think he'll do Yamaha as well though, they seem a pretty sorted lot.
Trefco (as mentioned above) - I have had services there as well, and I haven't ever had problems with my motors (2-stroke Mercs), but I have had some 'shoddy' workmanship with the untidy way they replaced my steering cables etc (this was sorted out though when I complained), but they are also not Yamaha agents.
Droomers - Voortrekker Rd, Bellville: I have no '"Boating" experience with them, but there motorcycle work has been good and I have seen them working on outboard motors in their workshop. They ARE yamaha agents as well. (m/cycles and marine)
The rest is in the S/Suburbs, but I have no experience of them. Not that I've had much of the above - my choice from the interaction I've had (not actual service) for you would probably be Magson's, simply due to them being around for so long, and I haven't heard negatives.
Good luck - hopefully someone can give you more "hands-on" advice.