http://tex.stackexchange.com/questions/38348/in-texshop-is-there-a-directive-to-select-biber-or-bibtex-on-a-per-document-bas
https://github.com/qubyte/BibDirective
The next feature was requested by Alan Munn about a year ago. Apologies for the delay. In the meantime, Mark Everitt wrote an ingenious script to provide this feature. The feature provided by that script is now built into TeXShop.
The command BibTeX in the TeXShop typeset menu runs BibTeX; notice that this command has a keyboard shortcut. In Japan, a different program is used instead, so Yusuke Terada provided an item in TeXShop Preferences under the Engine tab to select the program to be run when this menu item is selected. Examples are bibtex, biber, pbibtex, etc. The Preferences item can also be used to add flags to the command.
In TeXShop 3.21, the BibTeX engine can be selected on a file-by-file basis using the syntax
% !BIB TS-program =
The alternate syntax
% !BIB program =
will also be accepted. The item after the equal sign gives the name of the program (for instance biber) and any required flags. This line should be written within the first twenty lines of a source file.
The % !BIB TS-program = line takes precedence. If it is absent, the Preference item determines which command is run.