The V6 comes from Toyota's GR engine family. It's a fairly new engine. It's the successor to the MZ and VZ engine families. IMO, it's a great engine because Toyota designed from scratch to be a 4.0 and reduced bore and stroke to make smaller displacement versions, whereas other manufacturers usually start with a smaller displacement engine and increase bore and/or stroke to get a bigger displacement engine.
The 4.0 V6 in the 4Runner is the 1GR-FE. The 1GR made it's debut in the 4Runner in 2003. It was a brand new V6 for the 4th generation 4Runner. Currently the 1GR is found in the 4Runner, second generation Tacoma, FJ Cruiser and Tundra.
The GR family of engines includes the 2GR-FE (found on Camry, Avalon, Sienna, Highlander, RAV4, ES350, RX350 and upcoming Venza), 2GR-FSE (found on IS350 and GS350), 3GR-FSE (third generation GS300) and 4GR-FSE (IS250).
The 1GR only has VVT-i. The 2GR, 3GR and 4GR are dual VVT-i, meaning both the intake and exhaust cams are variable valve timing as well.
The applications above are for US models, additional information on the GR family can be found
Wikipedia.
On a side note, 2005 was powertrain upgrades for the 4th generation 4Runner. VVT-i was introduced on the V8, 2UZ-FE. The 4.0 V6 always had VVT-i, in 2005 it got a 5-speed automatic (same one as the V8, was a 4-speed in 2003-04).