In the BiomeGen class (not sure which one, the one where all the biomes are declared) there are some variables. If you set a new value to any of those in the @Init or @PostInit methods of your mod, the biomes will change accordingly. I have no idea how to explain it in another way.
biomeGenSky = new BiomeGenSwamp();
would be an example. However, I haven't looked into any biomes for some time, and I can't tell you for certain this will work. Good luck on finding your solution!
EDIT: I have been looking around for you, and here it is:
BiomeGenBase.*variable of biome you want to overwrite* = *value with which to overwrite*
For instance:
BiomeGenBase.biomeGenHell = new BiomeGenPlains();