Comparing SIFT and PolyPhen to other methods
I will strongly suggest you:

PredictSNP: It's the best tool for nsSNP detection as it compares and throw out result from all the tools available.

http://loschmidt.chemi.muni.cz/predictsnp/

Paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894168/