The best place to access the Mat-Su from the sea is...Anchorage. Palmer and Wasilla are only as significant as they are because they're suburbs/exurbs of Anchorage. The Mat-Su is a fairly marginal agricultural area and there's very limited agricultural potential in the interior. There is some farming on the Tanana around Fairbanks and Delta Junction, but it's basically on state-supported life support and it would be hard to imagine scenarios in which there would be more.
There's nothing of value on the Yukon below the junction with the Tanana and you have a long hazardous way to go from the river mouth to the Tanana. Accessing the Yukon overland is much more sensible, plus ships have a long way to go out of their way into the Bering Sea to get at it.
The Copper isn't navigable, Kennecott was accessed by rail from Cordova when the mines were active, though Valdez would have been equally possible. There is limited cattle ranching on the Copper, but agriculture isn't really possible.
I don't think you fully appreciate the climate and terrain challenges in Alaska. There are not virgin prairies out there in the permafrost awaiting eager pioneers. Alaska is very populous and developed compared to how things could have gone.
But Palmer and Wasilla are further inland than Anchorage along/near the Knik Arm, which means less transportation to the sea. Could a port further inland take the place of Anchorage?
What I'm visualising for Alaska is a scenario with an entirely different sort of colonisation than OTL. Parts of Russia (like Arkhangelsk, Transbaikalia), Sweden (Norrland), and Finland (Pohjanmaa) which have significant amounts of people have similar climates. Maybe medieval colonisation by a highly divergent Japan causes a more populous and different Alaska? Hardy Japanese peasants could eke out a living in certain areas growing barley and buckwheat (in later eras potato or even quinoa), with the economy later becoming much like Siberia's with extensive mining and fossil fuel extraction. Of course, aside from the problem of how Japan gets to that position, there's the problem that our Japanese explorers would inevitably find the much nicer lands of the Pacific Northwest leaving Alaska as simply a stop on a place to somewhere else. And a later 19th century Japan obtaining Alaska (which would be quite an achievement in diplomacy) probably wouldn't get the same results medieval colonisation might, although would result in a more populous Alaska earlier assuming an even harder US stance against Japanese immigration, eager Japanese efforts for colonisation (Karafuto and Nan'you gained a very large amount of Japanese relatively quickly, so in theory might Alaska amount to such, especially since it would have even more time?), and of course a Japanese government not willing to go for suicidal wars against the United States or British Empire. Essentially, Alaska would be Japan's Siberia in this case, and really in most any scenario of Japanese colonisation.
Oh, and seeming that many are mentioning US cities around here, let me ask:
In a scenario wherea advanced native american civilizations are more widespread, to the point of reaching the territory of the OTL USA (maybe a PoD in more north american creatures surviving the quaternary extinction process, with some becoming beasts of burden), which places do you think would be practical as capitals or entrepôts?
The Dalles, Oregon, was the site of one of the major trading centers for American Indians for thousands of years thanks to its place on a portage on the Columbia River. So it seems inevitable that it might be the site of considerable importance.
The historic outlets of the Mississippi are interesting. If you have an early enough civilisation which would need to include far-reaching maritime trade with Mesoamerica and the Caribbean, you might get a sizable center (an equivalent to New Orleans) along the Bayou Teche. After around 800 BC or so, the course of the Mississippi might stil change leaving the city along the Bayou Teche a village surrounded by impressive ruins as a new center along the Bayou Lafourche rises to replace it. Around 1,000 AD, the current course of the Mississippi will likely become established (barring some insane river control systems and some serious luck with floods, note that even the US can't stop the Mississippi from changing course without luck with flooding as we've had and very expensive modern engineering efforts), ensuring the quick decay of the civilisation in that area and the rise of a new major center around New Orleans/Baton Rouge.
A lot of major cities in the Eastern US are natural sites for major centers to build, since the same thing that made them so attractive to white settlers made them attractive to the American Indians before them. St. Louis is an obvious example, considering Cahokia and other mound complexes on the site. Nashville, Tennessee is another example, since the area had significant Indian settlement since there were Indians to begin with, as well as having a large population into the Mississippian period. The area has fertile land, is well watered, and has good river transportation links along the Cumberland and its tributaries. It would thus make for a suitable capital for a regional empire.
In general, the easiest way to discern potential major centers for more developed Native American civilisations is to look for areas where the archaeological record is extensive and archaeological sites are extensively clustered. Now, I don't think a Native American empire the size of the United States (even without Alaska) is possible unless we're talking about some sort of "North American Union" or something, since the region is simply too diverse (multiple centers of civilisation, just like the Old World) and too big for that too happen, unless you have it all be colonised by one power India/Indonesia style. Although IMO, I'd put the capital around St. Louis if we needed a capital of North America, since it's centrally located, especially if you have extensive improvements on the Missouri River to allow for navigation for large boats as far inland as Great Falls, Montana. The main problem with St. Louis is that it's right on the Great Plains, where as OTL demonstrates, is prime territory for a horse nomad culture which means it's in a similar position as Moscow or other centers of medieval Russia.