There are two ways to accomplish this. The first is
var mongoose = require('mongoose');
var myStub = sinon.stub(mongoose.Model, METHODNAME);
If you console log mongoose.Model you will see the methods available to the model (notably this does not include lte option).
The other (model specific) way is
var myStub = sinon.stub(YOURMODEL.prototype.base.Model, 'METHODNAME');
Again, the same methods are available to stub.
EDIT: Some methods such as save are stubbed as follows:
var myStub = sinon.stub(mongoose.Model.prototype, METHODNAME);
var myStub = sinon.stub(YOURMODEL.prototype, METHODNAME);
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