I use the air filter gate plug in that comes with pro tools. Use it as an insert and record to another track. The one draw back is that you can't automate the pattern or rate parameters so you may need to record several versions, and edit and layer them.
From there you process it using other plug ins (pitch shifters, time expansion/ compression etc.) to make the sound fit for what you need.
I recorded myself de-tuning a string on my guitar, and did one pass with the filter gate plug in. Check it out here-
http://soundcloud.com/dan2997/air-filter-gate-example