I'd go with the Flowmaster, but that's just me. I'm not a fan of flow-thru performance mufflers on 4 & 6 cylinder engines, but that's just me too - they just don't sound right to me and never have. My nephew has a Flowmaster setup on a V6 Ford Ranger...I don't care for the sound, but he loves it.
I do have Flowmaster mufflers on several of my rides though, both V8 powered. I have a SI/DO Flowmaster on my 2000 V8 Tundra that sounds mean, but with SI/DO it created its own x-pipe basically. Nice even pulses that growl, but is not obnoxious. I left the resonator in place on the Tundra too. Setup is going on 7 years old and is still in good shape, I don't think you can beat Flowmaster's quality - except with maybe Borla or Magnaflow. I have a Magnaflow setup on my Corvette that sounds awesome.
If you want to hear the differences, I think there are several YouTube videos out there that compare Vortex Cherry Bombs to some of the Flowmasters...I think I saw a link to a Vortex-equipped V6 4Runner listed on there in fact.