There are some scriptural justifications for different "levels" in Christianity, but it depends on what you mean by "levels". If you mean some places where Jesus is and some where He isn't, you'd be wrong. Heaven is nonsense if God isn't there. I think a much more reasonable (and hopefully more common) conception of different levels is different levels of reward, which I believe is very strongly based in scripture. Here's my list (all texts are NIV):
1 Cor 15:
39All flesh is not the same: Men have one kind of flesh, animals have another, birds another and fish another. 40There are also heavenly bodies and there are earthly bodies; but the splendor of the heavenly bodies is one kind, and the splendor of the earthly bodies is another. 41The sun has one kind of splendor, the moon another and the stars another; and star differs from star in splendor.
This is, in my opinion, one of the weaker texts, and I don't use it very much. I'm only including because it's one that I hear referenced very often. The idea is that different people's heavenly bodies have different levels of "splendor", which corresponds to their reward, or rank, or "level" in heaven.
Another good scripture is the entire description of the tabernacle of the Testimony (Ex 25-32? Around there). There is the outer court, the Holy Place, and the Most Holy Place. Since we know this is a shadow of the true tabernacle (See Hebrews), then we know that there must be an outer court, a Holy Place, and a Most Holy Place in heaven as well. These could also be construed (reasonably) as "levels".
Another couple good scriptures are the parables of the talents and minas, which I presume everyone knows and can find. In the parable of the minas in particular, we can see that the number of cities the first two faithful servants were given matched the number of minas they had. So we know from that, that different people are rewarded differently based on how much fruit they bear in this life. You might challenge this (since I'm not really developing the idea much or backing it up), but I'll just leave it out here.
Another good scripture about different rewards in heaven is 1 Cor 3:
10By the grace God has given me, I laid a foundation as an expert builder, and someone else is building on it. But each one should be careful how he builds. 11For no one can lay any foundation other than the one already laid, which is Jesus Christ. 12If any man builds on this foundation using gold, silver, costly stones, wood, hay or straw, 13his work will be shown for what it is, because the Day will bring it to light. It will be revealed with fire, and the fire will test the quality of each man's work. 14If what he has built survives, he will receive his reward. 15If it is burned up, he will suffer loss; he himself will be saved, but only as one escaping through the flames.
This clearly demonstrates that Christians (who are building on the foundation of Christ) can either build with things of value, or things of no value. You then know that some receive "his/her reward" and some "suffer loss", but are saved anyway. This is a clear differentiator, and could be construed as different "levels" of reward, depending on what you build with.
I could go on and on and on, but this is a pretty good foundation.
(I used to really dislike the notion of different rewards in heaven, since it seemed unbiblical to me as well, but the 1 Cor 3 and parts of 1 Cor 15 that I didn't reference really changed my mind on the subject. I've since found the other piles of verses)