UMD/AMD solution
For those guys, who are doing it through UMD, and compile via require.js, there is a laconic solution.
In the module, which requires tether as the dependency, which loads Tooltip as UMD, in front of module definition, just put short snippet on definition of Tether:
// First load the UMD module dependency and attach to global scope
require(['tether'], function(Tether) {
    // @todo: make it properly when boostrap will fix loading of UMD, instead of using globals
    window.Tether = Tether; // attach to global scope
});
// then goes your regular module definition
define([
    'jquery',
    'tooltip',
    'popover'
], function($, Tooltip, Popover){
    "use strict";
    //...
    /*
        by this time, you'll have window.Tether global variable defined,
        and UMD module Tooltip will not throw the exception
    */
    //...
});
This short snippet at the very beginning, actually may be put on any higher level of your application, the most important thing - to invoke it before actual usage of bootstrap components with Tether dependency.
// ===== file: tetherWrapper.js =====
require(['./tether'], function(Tether) {
    window.Tether = Tether; // attach to global scope
    // it's important to have this, to keep original module definition approach
    return Tether;
});
// ===== your MAIN configuration file, and dependencies definition =====
paths: {
    jquery: '/vendor/jquery',
    // tether: '/vendor/tether'
    tether: '/vendor/tetherWrapper'  // @todo original Tether is replaced with our wrapper around original
    // ...
},
shim: { 
     'bootstrap': ['tether', 'jquery']       
}
UPD: In Boostrap 4.1 Stable they replaced Tether, with Popper.js, see the documentation on usage.