Both are rated around the same HP and Torque.
Both have a strong aftermarket, however, I've heard of several performance complaints with the WS6.
Traveling around to an extremely large number of car shows and events last year, I'd tend to favor the Cobra 4.6 significantly more.
The number of Mustangs I saw with simple bolt on's that were pushing the 450-500+ HP range was quite substantial compared to those with LS1 TA's.
Combining that and my own experience with the 4.6L over the past 2 years, I have found these engines incredibly easy to increase power on.
My 95 Tbird with an OEM 225 HP 4.6L is now pumping out roughly 300 HP at the wheels with an aftermarket exhaust, ignition, Ported Intake and Throttle Body, Injectors, and a ECM upgrade.
Saleen, Roush, and Steeda, have all worked wonders with the 4.6.
Personally, I'd look that direction.....