Maybe not Maine, but some northern state.
Here's one possibility.
The "Lower 48" may have been created by residents of Alaska to denote the rest of the United States. The sources mention this idea only briefly, but it does provide a neat answer to your question--If the origin is Alaskan, then Maine is indeed "Lower." Hawaii is a bit more complicated, but the second source suggests, albeit briefly, that "The Lower 48 and Hawaii" isn't a terribly unusual designation, which would clear up any ambiguity.
There is the question of why this phrase is used throughout the US. First, it could be used wrongly--A dead link on Wikipedia supposedly pointing to a National Geographic style guide says that the term "Lower 48" should only be used in Alaskan contexts. Most likely the phrase has just worked its way into US culture and there's a bit of source amnesia. I mean, the phrase makes intuitive sense if you don't scrutinize it.
not really a substantive response to your question, but with regard to the northernmost point in the "lower 48": you're right, it's not maine
http://en.wikipedia.org/wiki/Extreme_points_of_the_United_States#Northernmost_points
"Note that maps of the 48 states that are displayed in a non-cylindrical projection (i.e. curved lines of latitude) can give the impression that the state of Maine extends farther north than it actually does. The northernmost point in Maine is at approximately 47.46 degrees North latitude. This line of latitude passes through the southern suburbs of Seattle. From there, it is approximately 100 miles (160 km) north to the 49th parallel. A wide swath of land within the 48 states (encompassing portions of Washington, Idaho, Montana, North Dakota, and Minnesota) is therefore farther north than any place in Maine."
there is a part of the "lower 48" that extends past the 49th parallel that marks much of the US-canada border, and it is in minnesota
I don't have my copy handy, and the libraries are closed for the night, so I'm going from memory on this. Refer to The Dictionary of Alaskan English.
In short, the term dates from before 1959, when there literally were 48 states. Hawaii was a territory, so it didn't factor into things. You also see "the States" mentioned in a similar context.
Incidentally, "going Outside" (capitalized O) is another common term, but it can be used for any Outside Alaska location, not just the United States.
It excludes Hawaii and Alaska because they aren't connected to any other states
This doesn't address your question specifically, but to clear up a common misconception: Minnesota actually has parts further north than Maine. But the earth is curved and maps are flat and usually centered in the Midwest, so people think Maine is further north.