The Spider-Man movie has taken more than $800m (£500m) at worldwide box offices and millions more from video and DVD sales - but Mr Lee says he has not seen a penny.
The 79-year-old - who worked for Marvel for more than 60 years - said he had an agreement with the publisher to get 10% of their profits from films and TV shows based on his creations.
Marvel has reported millions of dollars in earnings from the Spider-Man film - but no profits as defined by their contract.
As well as Spider-Man, Lee created the Incredible Hulk and X-Men characters.
He also wants a judge to ensure he gets a share of the takings from upcoming movies based on his characters, including a Spider-Man sequel, due in 2004.
The next film based on a Lee creation will be Daredevil, starring Ben Affleck. A Hulk film and X-Men sequel are also in the pipeline.
"Despite reaping enormous benefits from Mr Lee's creations, defendants have failed and refused to honour their commitments to him," the lawsuit says.
Marvel was "built on the wings" of his creation, the suit says, and Mr Lee put his trust in them.
Marvel executives have received "enormous windfalls" from the X-Men and Spider-Man films and merchandise, according to the lawsuit, which was filed at Manhattan federal court.
But Marvel said Mr Lee continued to be "well compensated" for his past contributions to the company and the comic book industry.
"Marvel believes it is in full compliance with, and current on all payments due under, the terms of Mr Lee's employment agreement and will continue to be so in the future," a statement said.
On Saturday, Lee was given one of the inaugural Golden Panel Awards by The New York City Comic Book Museum.
~RS~a~RS~International~RS~q~RS~~RS~z~RS~54~RS~)