Stan at Four Wheel Campers can and will answer your question - stan@fourwh.com
Tell him the year of the Eagle. The box probably is the same. The issue is the height of the bed rails. When we ordered our 2012 Eagle, we ordered it for a second gen Tacoma even though we mounted it on a first gen Tacoma (1999) for about a year. Bed rail height on second gen is higher.
You can also measure the distance between the bottom of the camper and the right (or left) angle section then compare with the bed rail measurement on the 2016 Tacoma.
Forgot to add......you may have to make a "ladder" type block to put between the bed and camper to raise the old one (pre- 2006) up to clear the bed rail.