will 16" rims from 3rd gen 4runner fit?

The back-spacing on the older Taco's is not as much as the 05+ Taco's, so they should fit no problem.

I recently sold my TRD off-road wheels and had numerous people interested who had older gen Taco's and I know they would not fit on the 1999 - 2000 due to too much back spacing.

They'd work fine. :thumbup:
Stock wheels on 3rd gen 4Runners (1996-2002) had +15mm offset.
Stock 6-lug wheels on 2nd gen Taco's (2005+) have +30mm offset.
So the 4Runner rims would have 15mm (0.59 inches) less backspacing, assuming equal wheel widths.
This means they would "stick out" further from your truck by that amount, which would look good IMO.