Lois can interbreed with Superman in Superman Returns.
Does that mean Superman is a subspecies of Homo Sapien?
http://en.wikipedia.org/wiki/Man_of_Steel,_Woman_of_Kleenex details the actual problems the two would have to overcome during sexual intercourse.
http://www.rawbw.com/~svw/superman.html is the actual text.
To summarise: it ain't gonna happen.
But that doesn't answer the question whether Kryptonians and humans are the same species. Of course being able to interbreed (which Niven states isn't possible) doesn't mean the two are of the same species. Interspecies crossbreeding is often performed in order to create hybrids between species. All it requires is a high enough level of genetic similarity between the species, which usually indicates a common ancestor not too far down the inheritance tree (e.g. a lion and a tiger afaik can be bred together, despite being different species).
So if the movie is correct in postulating that cross breeding the two is possible (despite the counter arguments as to the actual problems of performing such an act as presented by Niven), all we can ascertain is that they have a relatively recent common ancestor (which could hint at panspermia, the idea that life on different planets originates at the same point).
"Superman Returns" implied there is a measure of compatible genetic material between Humans and Kryptonians of a sufficient nature to allow offspring between the two. How viable the offspring of the two of them would be is never discussed.
Each movie continuity should be treated separately unless otherwise stated as a continuation of a previous movie or series.
While the idea of Human/Kryptonian hybrids was very popular in the Silver Age, the development of offspring between Humans and Kryptonians has been off the table since the DC Post-Crisis Man of Steel series by John Byrne.
NO, Humans and Kryptonians are not the same species, and given the genetic enhancements to the Kryptonian genome, it is unlikely (no matter what Superman Returns has shown) there could be any form of successful interbreeding between the two species without the help of advanced genetic manipulation technology.
Superman and Kryptonians in general, only share one characteristic with human beings; our external physical, bilaterally symmetrical appearance.
Kryptonians sufficiently resemble Humans enough for them to be able to pass as Human but only from a cursory physical inspection.
Any trained medical personnel should be able to determine a Kryptonian is not Human with only a modest toolkit of scientific equipment.
The only possible exception to this would be if the Kryptonians applied their transgenetic superhuman abilities once the child exited the womb/test tube. Then the possibility could exist that Humans and Kryptonians could be of similar species at the genetic level.
This idea is not as far-fetched as it initially might sound; the Kryptonians were inclined to develop their offspring in vitro (outside of the womb) using genetic technology. This has been part of the mythos since the very early Superman movies.
Despite the comic industry's belief that the Kryptonians would have developed their powers naturally, I stand by the idea that such powers were the result of technological enhancement in the distant Kryptonian past.
The technology which gives Kryptonians superpowers under a yellow sun were engineered, not born, no matter what has been written in texts because the range of such powers, the diversity and the specific defensive nature of those powers indicate a significant genetic enhancement program, not the random development of mutation, even after tens of thousands of years.
Such powers would make for formidable scouts, explorers and warriors. Since the worlds compatible with Kryptonians would likely be found around yellow stars, it is a logical development to ensure the successful establishment of colonies around such worlds.
Since 80% of the stars in our galaxy are red, it means around most stars, Kryptonians would have no superhuman abilities, increasing the possibility their powers were DESIGNED to give them an advantage on worlds compatible with their genome.
TL;DR: Most likely, the answer is "NO, different species", if we consider it in light of modern biology and "Species Problem".
Depends entirely on your definition of "species" (see "Species Problem" Wikipedia entry in detail).
Let's start with Wikipedia definition of "species" (emphasis and ellipses mine - DVK):
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring (Note: often, not always. Discussed below).
While in many cases this definition is adequate, the difficulty of defining species is known as the species problem. Differing measures are often used, such as similarity of DNA, morphology, or ecological niche.
Now, if we take simplistic
a group of organisms capable of interbreeding and producing fertile offspring definition, then Superman MAY be considered the same species as Lois... IF their children are fertile. As far as I'm aware from canon, merely having a child was the extent of the information, we don't know whether the child is fertile or sterile, so a weak "MAYBE" is the best we can do as an answer.
Now, that's of course not really how the messy science (and reality) of biology works. For example, we have genetic evidence that Homo Sapiens likely actually interbred with a different species, Homo neanderthalensis.
In addition, other interspecies hybrids are known to be fertile: Ligers (and even Tigons though the latter is iffy) are tiger+lion hybrids that can be fertile. Nevertheless, tigers and lions aren't even remotely the same species - meaning, even our original naive "MAYBE" answer turns to "likely NO, different species" if we consider what we know of modern biology.
If we take DNA (clearly Kryptonian DNA is different), morphology (the cells are WAY different since they give him non-human powers) or ecological niche (Krypton vs Earth), the answer is a firm "NO, different species"
It means that the writers wanted Lois and Clark to make babies, biological considerations be damned.
There's no reason to expect Kryptonian life to use the same molecular machinery for heredity that Earth life does; they may not use DNA at all, or if they do, their DNA may use different bases, or if they use the same bases, their genetic code may be different, etc., etc., etc.
There's no reason to expect that their naughty bits would be compatible with ours, or that their mechanism of reproduction would resemble ours in any way.
Now, convergent evolution is certainly possible; based on my very limited knowledge of physics and chemistry, I believe that any other life out there would at least be carbon-based and use many of the same compounds we do (we've found sugars, alcohols, and even amino acids floating around in space). There's a strong likelihood that, at the molecular level, things wouldn't be too alien. But replicating each other's evolutionary history to the point where we'd produce life forms that are similar enough to breed with each other? I don't want to think how many zeros are in that probability value.
Star Trek has the same problem all over the place (Spock, K'Ehleyr, Alexander, B'Elanna, all the Romulan-Klingon hybrids Worf found that one time, etc.). They tried to address it in canon, but frankly it's a mess all the way around.
To answer your question truthfully. Yes and no. Kryptonian and most humaniod race in fiction are essential evolved from the homo gene which technically make them sub species of humans. But the catch is kryptonian are advanced humans. That has been the origin since day one. Alien doesn't mean different species. It mean from outside that area. Thats why most humanoids can breed. Because they are essentially the same, meaning of the homo gene. But it doesn't always work out like that as dog and cats are said to come from the same ancestors. Its a loaded question. Also they have a son in comics too so that is canon.