It depends which boat you catch. Some of them go direct, others make a few stops but all on the Thalwil side of the lake so your ticket is still OK, and others zigzag back and forth to the Küsnacht side which would mean you'd need an extra ticket for that zone.
Best way to find out is to check the SBB website
. Enter Zürich Bürkliplatz and Thalwil ZSG, then go to "advanced search" and select only boats as your means of travel... this weeds out all those pesky tram-and-rail options.
Now, for whichever boat you're considering, click "Show intermediate stops". Your ticket needs to cover all the zones where those stops are located.
FWIW Zürich is actually the lower
end of the lake (the Limmat flows out, not in). The term "upper lake" or "Obersee" does exist, but it refers to the bit at the other end, past Rapperswil and Pfäffikon.