The JAWS AWS Module system (aka awsm) allows for this functionality via an attribute in the awsm.json metadata file that specifies how the lambda code is packaged.
Specifically the lambda.package.optimize.exclude and lambda.package.optimize.includePaths defined in the lambda configuration options section of the awsm.json spec.
The exclude attribute specifies node modules that should be excluded from the optimization process (under the covers it is just using browserify exclude). In the exclude attribute you simply specify ['aws-sdk']. You must then tell JAWS to include aws-sdk in the zip by putting its path in includePaths.
The includePaths attribute is a list of paths relative to the back directory that are pulled in as-is into the zip file before deployment.
For a complete example see the awsm sample