The two main marina areas are near Hayden Island (both on the island and on the "mainland") and the upper end of the Multnomah channel. You'll find the majority of the marinas in these two areas. In general, Hayden Island area has the more popular and upscale marinas, i.e., more expensive.
There are certainly other marinas scattered around the Portland area on the Columbia and Willamette. But before mentioning them, you need to decide:
-Where do you plan on cruising (or fishing) most?
-How far are you willing drive or how long of a commute are you willing to endure to get to your boat? Ex., if your marina is actually on Hayden Island and you want to get to it on a Friday after work.....traffic will make the process of getting to your boat miserable.
-Do you want covered, uncovered, or dry storage?
-How often do you plan on putting your boat on a trailer? If the your marina is not convenient to a boat ramp, it makes the logistics a bit trickier. Some marinas are within walking distance to a launch.
If you can answer some of these questions, it will help in determining which marina might work best for you.
I live 12 miles south of Portland so Hayden Island is not very convenient for me. I had a lot of work to do to my boat the first year I owned it so I wanted it close by. I chose to keep my boat at Sportcraft Landing in Oregon City. It's inexpensive ($166/mo, no charge for electric hookup), 9 miles from my house, covered, right next to a boat ramp, and has a fuel dock. On the negative side, it's in a fairly bad state of disrepair and nothing that will impress your friends or family. I'll most likely be moving my boat from there to Tyee Yacht club near Hayden Island now that I don't need to work on the boat every week.