The IRS publishes income tax data by zip code for certain years (1998, 2001, 2004-2008 etc.) but a) certain years are missing, like 1999 and 2000, and b) only for 2008 and afterwards are the data provided in CSV format (it's in the zip file) in a consistent format. Are these data available from elsewhere? I'm guessing they're not because in this question similar issues came up and people talked about how the IRS isnt really forthcoming about this. If nothing comes up here I'll try a phone call and see what they can provide me.
According to @MichaelA (in the comments), zip code level IRS income machine-readable income data is not available for every year, and the IRS has no plans to do so/isn't very receptive to the idea
You can get all the data based on county/city (not zip) for the years 1989-2010 here:
So not the exact format you asked for, but its something to work with and also covers the years you are missing and then some.
I took this data and scraped out the information for Virginia, which you can view here: