You should be able to set your Node version by overwriting the appropriate attribute.
Step 1-Create a custom cookbook for your project
Step 2- Create a opsworks_nodejs/attributes/customize.rb file.
Step 3- Set the following in that file
normal[:opsworks_nodejs][:version] = '6.0.0'
This has worked for me in the past (a couple years ago) - there's been some shift since then but it still should be the same...