Both the upper and lower river have really good bass fishing. In general, the upper river flows a little faster. There are more shallow spots on the upper river, the lower river tends to be more consistently deep.
I fish more on the lower river because it is closer to my house. It is a tidal river so be aware of that. On large tide swings there can be a 4' difference between low and high tide, often it is just a foot or two. I have a hard time saying whether I prefer an incoming or outgoing tide. Usually, the bass just bite when they feel like it.
Some good places to launch on the lower river would include Willamette part (across from Oaks park), Jefferson street or Cedaroak. Of those, I am most familiar with the Cedaroak launch and there is great bass fishing both up and downstream from there. That whole stretch has a lot of rocky banks that drop into deep water.
I have not spent as much time on the upper river, but I know for sure that there is good bass fishing out of Willamette park (where the Tualatin dumps in) and out of Roger's landing in Newberg. I see a lot of folks with bass boats launching from Wilsonville but I have never taken the kayak there.
I would recommend that you pick one area and try and learn it well rather than running all over the place looking for the magical hot spot. Any of those launches has tons of great bass water near them.