Many model years of Taco had multiple rim sizes. They went from 15" to 16" on the 4wd/prerunner models in 2001. But, if I 've got my facts right, in 2004 the 2wd model was still a 15" rim (and in 2005 for that matter).
In 1997 the 2wd came with a 14" rim and the 4wd with a 15" rim.
Citation:
http://www.customtacos.com/forum/16-2wd-wheels-tires/74917-2wd-5-lug-info-wheels.html
Tacoma's use a hub-centric wheel mounting. The way the spare mount works it only depends on the size of the opening in the rim. That center hole is also what centers the rim in a hub-centric setup, so it has to be right for the wheel to work properly anyway. So, if you get rims that work right on the taco, I'd put money that it won't matter at all if they are 15" or 16" rims.
That is... unless you upgraded your calipers/disks and 15" won't fit on the truck anymore, but again... that's whether they work when you mount them, it'd still carry fine as a spare (it just wouldn't be very useful).