Mike,
I don't think i saw it in the manual. However, it is a corporate policy for both Toyota and Lexus. You are allowed ONE free alignment. In fact, my '02 4Runner was out-of-balanced when i got it. Another Toyota dealer did the alignment for free.
If i were you, use the free alignment after you do some off-roading (if you're into that kind of stuff). Otherwise, just wait until you put more miles on your 4Runner.