You could create a dummy #include file of the following form:
#pragma once
#ifdef __INTELLISENSE__
void __syncthreads();
...
#endif
This should hide the fake prototypes from the CUDA and Visual C++ compilers, but still make them visible to IntelliSense.
Source for __INTELLISENSE__
macro: http://blogs.msdn.com/b/vcblog/archive/2011/03/29/10146895.aspx