A magnet school is a school with a specific focus - like a fine arts magnet or a military magnet or a vocational ed magnet. They would have a certain amount of funding set aside to pay for an enhanced curiculum. Usually they are still a public school and they follow all the rules of the public school system, they just have stuff "added". And they may or may have special enrollment requirements.
A charter school is a school that is 'run' by a corporation as a buisness and they recieve additional funding from that corporation. Even though it will have a principal and from the "outside" look like any other school - the actual decision making can be quite different. They are considered a public school and they have access to public funding therefore they can't exclude students (but if a charter school is good, it will have a wait list and may enroll based on a lottery). Charter schools don't have to adhere to all the public school requirements (for example length of the school day or union policies) but they do have to adhere to the testing requirements for your state in order to continue to receive public funding.
Either way you want to go to the school and check it out before enrolling your kids!
Hope that helps.
I just saw Tracy K's post - that is a fabulous link!!!!!!