If you're really serious about finding an answer OP I'd suggest ordering the following primary source: Internal Revenue Assessment Lists for Virginia, 1862-1866. It comes on 35mm microfilm, but it will probably have part of the answer you're looking for.
To provide a further answer, their was a tax of 5% on incomes between $600 and $5,000 that was in place until it was repealed in 1872. R.E. Lee's annual salary at Washington College was $1,500 a year when he accepted the job as President. I don't see a reason why he wouldn't have paid the 5% tax on his salary, but can only confirm this through the aforementioned documents.
http://www.civilwar.org/education/history/warfare-and-logistics/logistics/tax.html
C.B. Flood. "Lee's Last Years."
Robert e Lee signed a amnesty oath in 1865 and reluctantly took up the position of president of Washington college. There is no reason for him not to pay taxes.
http://www.pbs.org/opb/historydetectives/feature/lee-after-the-war/
http://en.m.wikipedia.org/wiki/File:Robert_E_Lee%27s_Amnesty_Oath_1865.gif
