I'm taking AP Computer Science this year, so I kind of know the basics pretty well. Anyway, last year in the Programming class at my school I found out that YouTube is your friend. Just watch some tutorials and you will be able to build a basic knowledge that way. Alternatively you could use http://www.codecademy.com/ to learn. It seems to be very good, but it teaches Javascript, not Java. The basics are the same in both languages, but the syntax is a bit different.
Now just to even start editing the code in MineCraft you will need a java decompiler (I recommend JD - GUI) and the program Eclipse. You can find tutorials for both of these on YouTube. After that, you are set, good luck.