It depends on your location; although, 1000km is too low a boundary even in the best cases. At high latitudes, where there is virtually no plasmasphere, the contribution above 1500-2000km or so is generally negligible; however, at the equator one would have to consider electron density out to the plasmapause region. This will also depend on time of day, season, geomagnetic activity, and solar activity. For your own reference, try creating a few electron density profiles with the Gallagher Plasmaspheric Model (an extension of the IRI). See the following for some codes: https://plasmasphere.nasa.gov/models/ These models can at least give you a rough feel to assess the significance of plasmaspheric TEC in the context of what you're interested in researching and provide a starting point.

There has been a considerable amount of work done by Andrew Mazzella and his colleagues on assessing the plasmaspheric contribution and effects on GPS observations. I would consult his work as well.

Thank you for those suggestions David, My apologies for the delay updating this post. I was preparing for AGU as I posted this question. 

I sent a request for the 2009 North American paper from Andrew Mazzella and received an immediate response. He also included a very nice seminar paper that summarized developments in GPS TEC measurements spanning 15 years leading to ground-based measurements of the plasmasphere electron content (PEC). I would recommend contacting him if you or anyone else following this question are interested. 1000 km seems to be a typical designation for the ionosphere/plasmasphere boundary, however I agree with your observations and will also use the link you sent to look at a few profiles myself. For mid-latitude, the median PEC altitude is also affected by solar flux. There is a nice comparison in Figures 5 (a&b) in the North American paper:  

Article (Mazzella_2009) Mazzela Jr., A. J. Plasmasphere effects for GPS TEC measurements in North America Radio Science, 2009, 44, 1-15.