As you've pointed out, oTool with -L is telling you that the libc++.1.dylib is being used from /usr/lib.
OSX development provides you with the command *install_name_tool*, which allows you to set the location of the required paths.
As an example, you'd use it something like this: -
install_name_tool -change /usr/lib/libc++.1.dylib /usr/local/lib/libc++.dylib <target file>
where the first path is the current path, the second is the one you want to change it to and the third is the file you're changing the paths for.