There is more than one message (theme) present in the book Lunch Money. For me, though, two main messages stand out.
One is the importance of hard work. Right from the start of the book, it is clear that Greg is a hard working little kid. He's good at making money, because he is able to find, see, and exploit niche markets. But without his devoted efforts, simply knowing those markets are there won't earn him anything. Greg works hard at making those markets his own. Even when competition stands in his way, Greg looks for ways to improve his product. Later, when the school administration works to shut him down, Greg tries to find ways to work within the system and keep his business open.
I think a second message of the book is the importance of team work. Greg and Maura could have stayed competitors, and they probably would have done okay. They might have both run their businesses into the ground, too, but they decided to work together. They made that decision because Greg and Maura saw that each of them had their own set of strengths that would make a combined business even stronger. As Greg and Maura learned the value of working together, they expanded their team to include Mr. Z. With his help, they were able to create a flourishing comic book business within the school.