Best tuner
 

I have a 99 F 250 LD with a 5.4, 3:73 gears with just over 100,000 miles on it. I tow some heavy loads during the summer.

What is the best tuner for more power while towing?

Unless Bill has something else this is about it:Power Hungry Performance - Phoenix 4-Position Chips

define heavy... a 5.4 gasser with 3.73 gears can't tow that much....those are highway gears when put in that lil engine.
are you asking between a Gryphon vs a multi position chip or between tuning brands.... I will say Bill's tunes are probably the safest around as far as not risking engine damage... A custom tow tune will probably be best for you but you will need to give us a lot more info on what you tow... any issues with towing or shifting now etc... then tell us what u want it to do....

In the summer about once a week I pull a gooseneck trailer with two tractors on it. The tractors weigh about 9000 pounds combined. Trips less than 100 miles one way.

I pulled 11,000 lbs from northern Vermont to Asheville NC down I81 at 15 mph in my F150 7700 5.4 7.73 with 285 75 16 tires. The truck pulls just fine.