After searching for the reason of error in the web I found this which explain about compiling boost with clang. I am not sure why adding define=BOOST_SYSTEM_NO_DEPRECATED made it worked. Please do comment anyone who knows why it worked. I was then able to compile with no error but I still see some warnings but it worked for me for now.
The default clang I am using is (clang-mp-3.3)
$ clang -v
clang version 3.3 (tags/RELEASE_33/final) Target: x86_64-apple-darwin11.4.2 Thread model: posix
./bootstrap.sh --with-toolset=clang --without-libraries=mpi,python,graph_parallel
./b2 clean
./b2 toolset=clang cxxflags="-std=c++11 -stdlib=libc++" linkflags="-stdlib=libc++" define=BOOST_SYSTEM_NO_DEPRECATED